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Insight IITurbomole

March 2000

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Copyright*

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Turbomole Contents–i

Table of Contents

APPENDICES

INDICES

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1–1

What Is Turbomole?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1–1Turbomole—The Insight® and Standalone Modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1–2Comparison of the Insight and Standalone Modes of Turbomole . . . . . . . . . . . . . . . . . . 1–3Starting Turbomole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1–3Using This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1–3Additional Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1–4Note on Documentation of Command Names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1–4

2. Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2–1

Geometry Optimization—The OPTIMIZE Suite of Algorithms . . . . . . . . . . . . . . . . . . . . 2–1Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2–1Theory and Implementation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2–4

The EF Algorithm and Mode Following . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2–4Constrained Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2–5GDIIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2–7

Density of States Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2–9

3. Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3–1

Organization of Turbomole. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3–1

4. Command Summary—The Insight Environment. . . . . . . . . . . . 4–1

Setup Pulldown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4–1Symmetry Pulldown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4–2Optimize Pulldown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4–2Background_Job Pulldown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4–2Run Pulldown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4–3

Contents–ii Turbomole

Table of Contents

Analyze Pulldown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4–3

5. Methodology—The Insight Environment . . . . . . . . . . . . . . . . . . . . .5–1

Using Turbomole in the Insight Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–1Outline of Basic Steps of a Turbomole Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–2

Step 1: Defining the Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–2Step 2: Setting up the Calculation Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–2Step 3: Performing the Turbomole Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–3Step 4: Analyzing the Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–3

Setting up Calculations with the Commands in the Turbomole Module . . . . . . . . . . . . . .5–3Beginning a Turbomole Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–3Defining the Molecule and Its Point-Group Symmetry . . . . . . . . . . . . . . . . . . . . . . .5–3

Specifying the System and Type of Calculation. . . . . . . . . . . . . . . . . . . . . . . . .5–3Finding and Adjusting the Molecular Point-Group Symmetry . . . . . . . . . . . . . .5–4

Finding the Point-Group Symmetry without Changing the Molecule’sGeometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–4

Imposing Exact Symmetry on the Molecule and Using Symmetry inCalculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–5

Technical Notes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–5Specifying Parameters that Control the Calculation. . . . . . . . . . . . . . . . . . . . . . . . .5–6

Using the Setup/Parameters Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–6Selecting the Calculation Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–6

Methods Available . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–6Choosing which Method To Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–7

Selecting the Basis Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–8Using the Basis Set Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–9Using Effective Core Potentials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–12Reading Basis Sets and ECPs from a User-Supplied File . . . . . . . . . . . .5–12

Controlling Disk and Memory Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–13Defining the Electronic State . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–14Setting up the SCF Portion of a Turbomole Job . . . . . . . . . . . . . . . . . . . . . . . .5–15Calculating Other Properties with Turbomole . . . . . . . . . . . . . . . . . . . . . . . . . .5–19Volumetric Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–20Using OPTIMIZE in the Insight Environment . . . . . . . . . . . . . . . . . . . . . . . . . .5–21Setting up Grid Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–27

Setting Up the Background Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–28Starting the Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–29Monitoring a Background Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–30Visual Aids to Analyzing Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–30

Displaying Orbital Contours . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–30Displaying Normal Mode Vibrations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–31Displaying Density-of-States Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–31Displaying a Summary of Turbomole Output . . . . . . . . . . . . . . . . . . . . . . . . . .5–31

Using Other Insight Pulldowns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5–32

6. Tutorial—The Insight Environment . . . . . . . . . . . . . . . . . . . . . . . . . . .6–1

Pilot Online Tutorials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6–1Overview of Tutorial Lessons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6–1

Turbomole Contents–iii

Table of Contents

7. Keywords Summary—Standalone Mode . . . . . . . . . . . . . . . . . . . . 7–1

Header Keywords (used for job identification purposes only) . . . . . . . . . . . . . . . . . . . . 7–1Primary Job Control Keywords. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7–1Additional Job Control Keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7–2DFT-Specific Keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7–3Keywords for Controlling the External Environment. . . . . . . . . . . . . . . . . . . . . . . . . . . . 7–3Keywords Controlling Calculation of Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7–3Keywords for SCF Tolerances and Convergence Control . . . . . . . . . . . . . . . . . . . . . . . 7–5Keywords for Control of Geometry Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7–5

8. Methodology—Standalone Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8–1

Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8–1Running a Turbomole Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8–1Restarting a Turbomole Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8–1

A. References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A–1

B. Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B–1

C. Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–1

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–1File Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–1The .input File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–2

Sample .input Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–3.turbo_archive (control) File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–7_route.csh File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–11Sample .sum File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–12.outmol File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C–17

D. Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D–1

Background Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D–1

E. Commands—Standalone Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–1

Turbomole .input file. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–1Format for Documenting Turbomole Keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–7Detailed Descriptions of Keywords/Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–8

Contents–iv Turbomole

Table of Contents

ACM_Coeffs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–8AO_Integral_Filesize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–9Basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–10Basis_Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–25Boys_Localization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–26Calculate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–26Charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–28CONSTRAINT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–28Constraint_Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–29Damping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–30DIIS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–31Displacement_Convergence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–32ECP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–32ECP_Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–33Electric_Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–34Electrostatic_Moments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–35ESP_Charges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–36Excitation_Energy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–36Excited_State_Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–37Excited_State_Multiplicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–38Excited_State_Symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–38FIXED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–39Freq_Dep_Polarizability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–40Frequencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–40Functionals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–41GDIIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–42Geometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–43Gradient_Convergence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–50Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–51Hessian_File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–52Hessian_Update . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–52Integration_Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–53Level_Shift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–54Locate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–55Loewdin_Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–55Max_Core_Memory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–56Max_Displacement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–56Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E–57

Turbomole Contents–v

Table of Contents

MO_Guess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–58MO_Integral_Filesize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–58Mulliken_Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–59Multiplicity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–60NMR_Shielding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–60Number_Of_Excited_States. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–61Opt_Coordinate_System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–61Opt_Cycles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–62Opt_Energy_Convergence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–62Opt_Use_Symmetry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–63Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–64Point_Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–66Product. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–68Relativistic_Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–68Roby_Davidson_Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–69SCF_Density_Convergence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–69SCF_Energy_Convergence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–70SCF_Iterations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–70Spin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–71Static_Polarizability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–72Step_Size. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–72Swap_Alpha_Orbitals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–73Swap_Beta_Orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–73Swap_Orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–74Symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–75Title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–76Version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .E–76Index of Keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Keywords–1Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Index–1

Contents–vi Turbomole

Table of Contents

Turbomole 1–1

Introduction

1 Introduction

What Is Turbomole?

Turbomole is a software tool for the chemist, which can be used alone or in conjunc-tion with other Biosym/MSI software, to study the chemistry and physical propertiesof molecules in both materials and life science applications. Specifically, Turbomoleis a general-purpose, ab initio quantum chemistry program package designed for theprediction of molecular energies, structures, spectra, reactivity, and properties.

Turbomole was originally developed by Prof. R. Ahlrichs and coworkers at KarlsruheUniversity. Presently, development of Turbomole is ongoing through the combinedefforts of Prof. Ahlrichs’ laboratory and Biosym/MSI.

The current capabilities of Turbomole are summarized in Table 1–1.

Table 1–1. Capabilities of Turbomole (Page 1 of 2)

FunctionalityHFa DFTb MP2c

Rd ROe Uf Rd Uf Rd ROe Uf

Calculation of atomic and molecular energies. Yes Yes Yes Yes Yes Yes No NoCalculation of forces (energy 1st derivatives). Ag A A A A A No NoLocation of stable molecular geometries and transition state

geometries using automatically generated natural internalcoordinates.

Yes Yes Yes Yes Yes Yes No No

Calculation of molecular force constants and dipole deriva-tives (energy 2nd derivatives) for vibrational spectra.

A Nh N A/Ni A/N N No No

Calculation of electrostatic polarizabilities and 1st hyper-polarizabilites.

A No No No No No No No

Calculation of frequency dependent polarizabilities. A No No No No No No NoCalculation of NMR chemical shielding tensors. A No No No No No No NoCalculation of UV/visible spectra. Yes No No No No No No NoCalculation of dipole moment. Yes Yes No Yes No Yes No NoCalculation of higher electrostatic moments. Yes Yes No Yes No No No NoElectron population analyses. Yes Yes No Yes No No No No

1–2 Turbomole

Turbomole—The Insight® and Standalone Modes Introduction

Intro

duct

ion

Turbomole—The Insight® and Standalone Modes

Turbomole can be run in a standalone mode or as an application within the Insight IIgraphical molecular modeling interface, which is available from Biosym/MSI underseparate license.

When purchased with the Insight program, Turbomole is accessible as one of theInsight program’s modules. (For more information on the basic operations, proce-dures, and functionality of the Insight program, please refer to the Insight documen-tation.) The functionality in Turbomole is accessed through pulldowns that contain thecommands to set up a Turbomole job. The parameter block for each command pro-vides many useful defaults as well as preset strategies, all of which can be easily mod-ified for your particular calculation. References to atoms or residues during moleculebuilding or geometrical analysis can be typed in or can be specified by picking theappropriate atom or residue in the displayed structure. You can then start the run whileremaining in the Insight environment.

The parameter blocks in the Insight program can also be used to prepare input files forrunning Turbomole in the standalone mode. These input files can be edited to developmore sophisticated simulation strategies.

Finally, Turbomole can be set up and run completely as a standalone program outsidethe Insight environment (see Chapters 7 and 8).

aCalculations based on Hartree–Fock theory (see Chapters 2, 3).bCalculations based on density functional theory (see Chapters 2, 3).cCalculations based on Moller-Plesset perturbation theory (see Chapters 2, 3).dCalculations using a restricted spin wavefunction (see Chapters 2, 3) for molecules (or atoms) which areclosed-shell (all electrons spin-paired).eCalculations using a restricted open-shell spin wavefunction (see Chapters 2, 3) for molecules (or atoms) whichare open-shell (at least one electron is not spin-paired).fCalculations using an unrestricted open-shell spin wavefunction (see Chapters 2, 3) for molecules (or atoms)which are open-shell (at least one electron is not spin-paired).gDerivatives calculated analytically.hDerivatives calculated numerically.iCalculated analytically for local density functionals, numerically otherwise.

Inclusion of external electrostatic field and/or external pointcharges.

Yes Yes Yes Yes Yes No No No

Inclusion of effective core potentials. Yes Yes Yes Yes Yes Yes No NoHybrid quantum mechanics/molecular mechanics calcula-

tions.Yes Yes Yes Yes Yes Yes No No

Table 1–1. Capabilities of Turbomole (Page 2 of 2)

FunctionalityHFa DFTb MP2c

Rd ROe Uf Rd Uf Rd ROe Uf

Turbomole 1–3

Introduction Comparison of the Insight and Standalone Modes of Turbomole

IntroductionComparison of the Insight and Standalone Modes of Turbomole

Running Turbomole in the Insight environment provides you with advanced tools forbuilding, editing, and manipulating 3D molecules and for creating input files and jobscripts through command menus (“parameter blocks”). Additionally, the Insight pro-gram provides graphical tools for analyzing the results of your Turbomole calcula-tions:

• Contouring and coloring electron density, electrostatic potential, and molecularorbitals.

• Animating normal modes of vibration.

• Creating plots of orbital energies and density of states.

However, not all the features and capabilities of Turbomole are accessible through theInsight program. For this reason, it can be advantageous for advanced Turbomoleusers to first create the molecule, input file, and job script file within the Insight pro-gram, then leave the Insight program and edit these files by hand. Specifically, whenTurbomole is run from the Insight interface:

• Basis set and ECP assignment is less flexible.

• Nondefault values for many of the infrequently modified computational optionscannot be selected.

Starting Turbomole

Turbomole can be invoked by selecting Turbomole from the Module pulldown in theInsight program (the Module pulldown is accessed by clicking the Biosym logo). Sev-eral new pulldowns appear on the lower menu bar: Setup, Symmetry, Optimize,Background_Job, Run, and Analyze. Most of the commands in these Turbomolepulldowns are actually used to set up the control file for the job—Turbomole is notactually run until the Run/Run_Turbomole command is executed.

You can also set up and run Turbomole independent of the Insight interface by issuingthe following command at the UNIX prompt (see Chapter 8):

> turbomole run_name

Using This Guide

General informa-tion

This guide contains instructions for preparing input files, running jobs, and interpretingoutput. Chapters 1–3 and Appendices A–D contain information that is relevant to boththe Insight and standalone modes of using Turbomole. Chapter 1 is a general intro-duction to Turbomole and its documentation. Chapters 2 and 3 outline the theory and

1–4 Turbomole

Additional Information Introduction

Intro

duct

ion

its implementation, respectively. Appendix A contains the scientific references cited inthis guide, and Appendix B contains a glossary of terms and symbols. The file formatsare documented in a separate File Formats book for files used by more than one pro-gram and in Appendix C for those specific to Turbomole, and background jobs (as runfrom the Insight program) are documented in Appendix D.

Turbomole inthe Insight inter-face

Chapters 4–6 contain information that is specific to using Turbomole in the Insightenvironment. Chapter 4 briefly summarizes the main functions of each command.Chapter 5 explains how to use Turbomole in the Insight mode, and Chapter 6describes several tutorials that show you how to use it.

Turbomole instandalone mode

Chapters 7 and 8 and Appendix E contain information that is specific to using Turbo-mole in the standalone mode. These chapters are mainly of interest to more advancedusers, but are helpful for understanding how the computational work of Turbomoleactually occurs, whether it is run in the standalone mode or via the Insight interface.Chapter 7 lists and briefly explains all the keywords used in the standalone mode.Chapter 8 gives an overview of how to run Turbomole. Appendix E is a detailed expla-nation of the keywords and requirements of the computational routines of Turbomole.

Additional Information

In addition to this printed Turbomole documentation, on-line help is available in theInsight program and is activated by clicking the help icon, which is the button contain-ing a question mark, along the left side of the main Insight window. The help utilityallows you to print out formatted versions of the help files.

Information pertaining specifically to the Insight interface and its default modules iscontained in the Insight documentation. The formats of files that are relevant to morethan one Biosym/MSI product are documented in a separate File Formats book.

Technical information that is mainly of use to programmers and system administratorsis contained in the System Guide.

Note on Documentation of Command Names

In referring to commands that are used when running Turbomole through the Insightinterface, this guide uses the format Pulldown/Command, since you use the mouse toselect the pulldown first, before the command name appears. Note, however, that if youenter commands in the command area near the bottom of the Insight window, the com-mand names must be entered in the format Command Pulldown or Command(whichever appears at the top of the equivalent parameter block).

For conventions used in documenting the standalone commands, please seeAppendix E, Commands—Standalone Mode.

Turbomole 2–1

Theory2 Theory

This chapter summarizes the chemical and mathematical theory upon which Turbo-mole is based. An outline of how it is implemented in the program is contained inChapter 3.

Geometry Optimization—The OPTIMIZE Suite of Algorithms

Introduction

Turbomole includes a powerful suite of algorithms for geometry optimization, referredto collectively as OPTIMIZE. Within the Insight environment, you can control OPTI-MIZE via parameters in the Optimize/Opt_Parameters command.

After this introductory section, the theory behind the principal algorithms in OPTI-MIZE is presented, starting on page 2–4. (This section can be skipped by those whosesole interest is how to use the program.) Chapter 5, Methodology—The Insight Envi-ronment, includes a discussion of input parameters, options, and how to use OPTI-MIZE within the Insight interface. Lessons demonstrating how to use the Optimize/Opt_Parameters command are supplied electronically as Pilot tutorials.

What OPTIMIZEis and does

OPTIMIZE is a general geometry-optimization package for locating both minima andtransition states on a potential energy surface. It can optimize in Cartesian coordinatesor in a nonredundant set of internal coordinates that are generated automatically frominput Cartesian coordinates. It also handles fixed constraints on distances, bond angles,and dihedral angles in Cartesian or (where appropriate) internal coordinates.

The process is iterative, with repeated calculations of energies and gradients and cal-culations or estimations of Hessians in every optimization cycle until convergence isattained (see scheme in Figure 2–1). The whole art of geometry optimization lies incalculating the step h so as to converge in as few such cycles as possible.

Ease of use OPTIMIZE is designed to operate with minimal user input. All you need to provide isthe initial geometry in Cartesian coordinates (obtained from the Insight or Discoverprograms or from an appropriate database), the type of stationary point sought (mini-mum or transition state), and details of any imposed constraints. All decisions as to theoptimization strategy—how to handle the constraints, whether to use internal coordi-nates, which optimization algorithm to use—are made by OPTIMIZE.

2–2 Turbomole

Geometry Optimization—The OPTIMIZE Suite of Algorithms Theory

Theo

ry

You may, of course, override the default choices and force a particular optimizationstrategy, but there is no need to provide OPTIMIZE with anything other than the min-imal information outlined above. In particular, you do not need to provide, for exam-ple, a Z-matrix or other connectivity data in order to take advantage of the potentialefficiency gains associated with the use of internal coordinates. An excellent set of nat-ural internal coordinates (Fogarasi et al. 1992, Baker 1993) can be generated automat-

Figure 2–1. Schematic of Geometry Optimization by OPTIMIZE Set ofAlgorithms

Input initial geometry x(best guess at molecular structure)

Choose coordinate system best

Calculate energy E

Calculate gradient vector, g(first derivative of E with respect

Estimate or calculate Hessian matrix, H(second derivative of E with respect

From E, g, and H, calculate a new step, h(x = x + h should be a better estimate of the

Check for convergence(i.e., are energy differences, gradients, and

YES

Converged

suited for desired optimization

to coordinate displacement)

to coordinate displacement)

location of the stationary point sought than x was)

displacement less than desired tolerances?)

NO

Take new step

Turbomole 2–3

Theory Geometry Optimization—The OPTIMIZE Suite of Algorithms

Theoryically from the input Cartesians, and the optimization can be carried out using thesecoordinates.

Eigenvector fol-lowing

The heart of the program (for both minimization and transition-state searches) is theEF (eigenvector-following) algorithm (Baker 1986). The Hessian mode-followingoption incorporated into this algorithm is capable of locating transition states by walk-ing uphill from the associated minima. By following the lowest Hessian mode, the EFalgorithm can locate transition states, starting from any reasonable input geometry andHessian.

DIIS acceleration An additional option available for minimization is GDIIS, which is based on the wellknown DIIS technique for accelerating SCF convergence (Pulay 1982).

Constrained opti-mizations

The strategy adopted for constrained optimization depends on the starting geometryand the nature of the constraints. Constraints can be handled easily in internal coordi-nates, provided that (1) the constrained parameter (distance, angle, or dihedral) is a nat-ural part of the coordinate set and (2) the constraint is rigorously satisfied in the startingstructure. If both (1) and (2) hold for all desired constraints, then OPTIMIZE carriesout the optimization in internal coordinates. Otherwise, the constrained optimizationis performed in Cartesian coordinates.

Good Hessianleads to efficientoptimization inCartesian space

Traditional wisdom has it that optimization in Cartesian coordinates is inefficient rel-ative to internal coordinates; however, recent work (Baker and Hehre 1991) has clearlydemonstrated that, if a reasonable estimate of the Hessian matrix is available (e.g.,from a molecular mechanics forcefield) at the starting geometry, then optimizationdirectly in Cartesian coordinates is as efficient as an internal coordinate optimization.In particular, constrained optimization can be handled in Cartesian coordinates as effi-ciently as with a Z-matrix, with the additional advantages that any distance, angle, ordihedral constraint between any atoms in the molecule can be dealt with (i.e., there isno formal connectivity requirement), and the desired constraint does not have to be sat-isfied in the starting structure.

Lagrange multi-plier algorithm

OPTIMIZE incorporates a very accurate and efficient Lagrange multiplier algorithmfor handling constraints in Cartesian coordinates, with a more robust (but less efficient)penalty function algorithm as a backup. Both algorithms are suitably modified versionsof the basic EF algorithm (Baker 1992). The Lagrange multiplier code can locate con-strained transition states, as well as minima.

The original Lagrange multiplier algorithm has been significantly enhanced, to incor-porate both fixed and dummy atoms (Baker and Bergeron 1993). Standard distance andangle constraints can be specified with respect to dummy atoms, greatly extending therange of constraints that can be handled. Fixed atoms can be eliminated from the cal-culation (since there is no need to calculate their gradients), resulting in potentially sig-nificant savings of CPU time in ab initio computations.

2–4 Turbomole


Theo

ryTheory and Implementation

The EF Algorithm and Mode Following

Shifting the New-ton–Raphsonstep to favor opti-mization along aneigenmode

Mode following is a powerful technique for geometry optimization. It involves modi-fying the standard Newton–Raphson step:

Eq. 2–1

by introducing a shift parameter λ so that (Cerjan and Miller 1981):

Eq. 2–2

In terms of a diagonal Hessian representation, this can be written:

Eq. 2–3

where the ui and bi are the eigenvectors and eigenvalues of the Hessian matrix H, and = ut

i g is the component of g along the local eigenmode ui. Scaling the Newton–Raphson step in this way has the effect of directing the step to lie primarily (but notexclusively) along one of the local eigenmodes, depending on the value chosen for λ.

How the EF algo-rithm chooses theshift parameter

Various recipes for choosing a suitable shift parameter exist: the EF algorithm utilizesa rational function approximation to the energy, yielding an eigenvalue equation of theform (Banerjee et al. 1985):

Eq. 2–4

from which a suitable λ can be obtained. This RFO matrix equation has the followingimportant properties:

1. The (n + 1) eigenvalues of Eq. 2–4 {λi} bracket the n eigenvalues {bi} of the Hes-sian matrix λi ≤ bi ≤ λi+1.

2. At convergence to a stationary point, one of the eigenvalues of the RFO matrix iszero and the other n eigenvalues are those of the Hessian at the stationary point.

3. For a saddlepoint of order m the zero eigenvalue separates the m negative and(n - m) positive Hessian eigenvalues.

h H 1– g–= F x( ) 1–∇ 2 Fx∇≡

h H λ1–( ) 1– g–=

hFiui–

bi λ–-------------

i 1=

n

∑=

Fi

H g

gt

0

h

1

λh

1

=

Turbomole 2–5


TheoryEF enables bothminimization andtransition-stateoptimization

Property 3—the separability of the positive and negative Hessian eigenvalues—allowstwo shift parameters λp and λn to be used, one for modes along which the energy is tobe maximized and the other for which it is minimized. Specifically, for a transitionstate (a saddlepoint of order 1) in terms of the Hessian eigenmodes, we have the twomatrix equations:

Eq. 2–5

Eq. 2–6

where it is assumed that maximization is along the lowest Hessian mode bi. Note thatλp is the highest eigenvalue of Eq. 2–5—it is always positive and approaches zero atconvergence—while λn is the lowest eigenvalue of Eq. 2–6—it is always negative andagain approaches zero at convergence.

Choosing these values of λ gives a step that attempts to maximize along the lowestHessian mode and minimize along all the others. It always does this regardless of theeigenvalue signature (unlike the standard Newton–Raphson step). The two shiftparameters are then used in Eq. 2–4 to give a final step:

Eq. 2–7

This step may be further scaled down if it is considered too long. For minimization,only one shift parameter λn would be used and this would act on all modes. It is oftenpossible to locate different transition states from the same starting structure by maxi-mizing along a mode other than the lowest (hence “mode following”).

Constrained Optimization

Lagrange multipli-ers as constraints

The essential problem in constrained optimization is to minimize a function of, say, nvariables F(x) subject to a series of m constraints of the form Ci(x) = 0, (i = 1 … m).This can be handled by introducing the Lagrangian function (Fletcher 1981):

b1 F1

F1 0 h1

1

λp

h1

1

=

b2 0 F2... ...

0 bn Fn

F2 … Fn 0

h2...

hn

1

λn

h2...

hn

1

=

hF– 1u1

b1 λp–( )------------------------

Fiui

bi λn–( )-----------------------

i 2=

n

∑–=

2–6 Turbomole


Theo

ry

Eq. 2–8

which replaces the function F(x) in the unconstrained case. Here, the λi are the so-called Lagrange multipliers, one for each constraint Ci(x). Taking the derivative ofEq. 2–8 with respect to x and λ gives:

Eq. 2–9

and:

Eq. 2–10

At a stationary point of the Lagrangian function, we have ∇ L = 0, that is, all∂L ⁄ ∂xj = 0 and all ∂L ⁄ ∂λi = 0. This latter condition means that all Ci(x) = 0, and so allconstraints are satisfied. Hence, finding a set of values (x, λ) for which ∇ L = 0 gives apossible solution to the constrained optimization problem in precisely the same thingas finding an x for which g = ∇ F = 0 gives a solution to the corresponding uncon-strained problem.

EF and con-strained optimiza-tions

We can implement mode following in constrained optimization by simply adoptingEq. 2–4, but with H replaced by ∇ 2L and g replaced by ∇ L. However, it is importantto realize that each constraint introduces an additional mode to the Lagrangian Hessian(∇ 2L), which has negative curvature (a negative Hessian eigenvalue). Thus, when con-sidering minimization with m constraints, you should look for a stationary point of theLagrangian function whose Hessian has m negative eigenvalues, that is, for a saddlepoint of order m.

Insofar as mode following is concerned then, assuming a diagonal Lagrangian Hessianrepresentation, Eqs. 2–5 and 2–6 for an unconstrained system should be replaced bythe following for a constrained system:

Eq. 2–11

L x λ,( ) F x( ) λ iCi x( )

i 1=

m

∑–=

xj∂∂L

xj∂∂

F x( ) λ i xj∂∂

Ci x( )

i 1=

m

∑–=

λ i∂∂L

Ci x( )–=

b1 0 F1... ...

0 bm Fm

F1… Fm 0

h1...

hm

1

λp

h1...

hm

1

=

Turbomole 2–7


Theory

Eq. 2–12

where now the bi are the eigenvalues of ∇ 2L with corresponding eigenvectors ui and

= uti ∇ L. Constrained transition-state searches can be carried out by selecting one

extra mode to be maximized in addition to the m constraint modes, that is, by searchingfor a saddlepoint of the Lagrangian function of order m + 1.

GDIIS

In the GDIIS method, geometries (xi) generated in previous optimization steps are lin-early combined to find the “best” geometry on the current cycle (Császár and Pulay1984):

Eq. 2–13

Finding appropri-ate coefficientsfor use in GDIISmethod

The problem here, of course, is to find appropriate values for the coefficients Ci.

If we express each geometry (coordinate vector) by its deviation from the sought finalconverged geometry xf, that is, xi = xf + ei, then it is obvious that if the conditions:

Eq. 2–14

and:

Eq. 2–15

are satisfied, then the relation:

Eq. 2–16

also holds.

bm 1+ 0 Fm 1+... ...

0 bm n+ Fm n+

Fm 1+ … Fm n+ 0

hm 1+...

hm n+

1

λn

hm 1+...

hm n+

1

=

Fi

xn Cixi

i 1=

m

∑=

R Ciei∑ 0= =

Ci∑ 1=

Cixi∑ xf=

2–8 Turbomole


Theo

ryError vectors The true error vectors ei are, of course, unknown. However, they can be approximated

by:

Eq. 2–17

where gi is the gradient vector corresponding to the geometry xi. Minimization of thenorm of the residuum vector (Eq. 2–14), together with the constraint equation (Eq. 2–15), leads to a system of m + 1 linear equations:

Eq. 2–18

where Bij = ⟨ei ej⟩ is the scalar product of the error vectors ei and ej, and λ is aLagrange multiplier.

Calculating theintermediategeometry and itsgradient

The coefficients Ci determined from Eq. 2–18 are used to calculate an intermediateinterpolated geometry:

Eq. 2–19

and its corresponding interpolated gradient:

Eq. 2–20

Relaxing theintermediategeometry

A new, independent geometry is generated by relaxing the interpolated geometryaccording to:

Eq. 2–21

Modifications ofthe original GDIISalgorithm

In the original GDIIS algorithm, the Hessian matrix is static, that is, the original start-ing Hessian remains unchanged during the entire optimization. However, updating theHessian at each cycle generally results in more rapid convergence, and this is thedefault in OPTIMIZE. Other modifications to the original method include limiting thenumber of previous geometries used in Eq. 2–13 by neglecting earlier geometries and

ei H 1– gi–=

B11 B12 … B1m 1

B21 B22 … B2m 1... ... ... ...

Bm1 Bm2 … Bmm 1

1 1 … 1 0

C1

C2...

Cm

λ–

0

0...0

1

=

x ′m 1+ Cixi

i 1=

m

∑=

g ′m 1+ Ci gi

i 1=

m

∑=

xm 1+ x ′m 1+ H 1– g ′m 1+–=

Turbomole 2–9

Theory Density of States Graphs

Theoryeliminating any geometries more than a certain distance (default = 0.3 au) from thecurrent geometry.

Density of States Graphs

Once a converged electron density has been calculated, there are several ways to ana-lyze the results, in particular the wavefunction. A convenient way of displaying themolecular orbital spectrum is by constructing and plotting the density of states. Formolecular systems, this is commonly done by graphing the molecular orbitals as afunction of the MO eigenvalues. The degeneracy of the orbitals is then indicated by theheight of the functions. The expression used is a simple sum of delta functions:

Eq. 2–22

For analysis of metallic systems, some sort of artificial broadening is usually appliedto the DOS plot. This results in a better match with experimental data obtained frommethods like UPS and XPS. Two common ways of doing this are Gaussian broadeningand Lorentzian broadening. For Gaussian broadening every energy level is convolutedwith a function like:

Eq. 2–23

For Lorentzian broadening we use the function:

Eq. 2–24

The sigma parameter indicates the width of the peaks. For sigma values approachingzero, we obtain the delta representation from Eq. 2–22. The value of sigma is typicallyvaried so as to best represent the available experimental data.

Partial density of states (PDOS), also called local density of states, can be used to studythe contribution of a particular orbital or group of orbitals to the molecular orbital spec-trum. These methods are based on different population analysis schemes such as theMulliken and Loewdin methods.

The simplest form of calculating the PDOS spectrum is by projecting the atomic wave-function onto the molecular orbitals:

Dd E( ) E Ei–( )δi

∑=

Dg E( ) expE Ei–

σ--------------–

i 1=

N

∑=

De E( ) αEi E–( ) 2 σ2+

-------------------------------------

i 1=

N

∑=

2–10 Turbomole

Density of States Graphs Theory

Theo

ry

Eq. 2–25

This does give a reasonable indication of the contribution of that AO to the MO, but amajor disadvantage is that the values are not normalized. Adding up the partial DOSfor all orbitals in the system does not add up to the total number of electrons of the sys-tem, because of the non-orthogonality of the basis functions on different atoms.

The Mulliken and Loewdin analyses are different methods that circumvent this prob-lem. For Mulliken analysis the PDOS is defined as:

Eq. 2–26

where Dij is the AO density matrix. This definition allows the Mulliken density ofstates to become negative. The Loewdin analysis does not have this drawback, since italways gives positive values because of its definition:

Eq. 2–27

where Sif = ⟨ φi | φi ⟩ and S1/ 2 is the square root of the overlap matrix S. However, weshould stress that these different population analysis methods are all somewhat arbi-trary, due to the partitioning of S, and care should be taken in attributing too muchphysical significance to them.

Dj E( ) φj ψi⟨ | ⟩ E Ei–( )δ ni–

i 1=

N

∑=

Dj E( ) φj φi⟨ | ⟩ Dij E Ej–( )δ

i 1=

N

∑=

Dj E( ) Sjk1 2⁄

DkiSij1 2⁄

E Ej–( )δ

ik

N N,

∑=

Turbomole 3–1

Implem

entation

3 Implementation

This chapter outlines the structure and interrelationships of Turbomole and its constit-uent programs.

Organization of Turbomole

Turbomole is composed of several separate executable modules and scripts, each ofwhich carries out a specific task in your Turbomole calculation. The control andorchestration of the separate Turbomole executables and scripts is carried out by the C-shell script called turbomole. The turbomole script thus determines which modulesneed to be executed (and in which order), based on the information in your run_name.input file.

Technical Note: The Turbomole executables are located in:

$BIOSYM/$BIOSYM_PLATFORM/biosym_exe/

while the scripts are located in:

$BIOSYM/biosym_bin/

Proper installation of the Biosym/MSI media should have added these two directoriesto your path. However, if the directories do not appear in your path, you will need toadd them by hand. For information about the UNIX $path variable, refer to your UNIXmanual or consult your system administrator.

The tasks performed by each of the modules are summarized in the following list:

• NumFREQ performs finite-displacement, numerical 2nd derivative calculations.

• OPTIMIZE performs geometry optimization.

• TurboFREQ calculates SCF 2nd derivatives (vibrational frequencies + IR intensi-ties).

• TurboGEOM sets up molecular geometry and symmetry.

• TurboGRAD calculates SCF 1st derivatives (forces).

• TurboGUESS generates initial SCF MOs and orbital occupations.

• TurboMPGRAD calculates MP2 energy, calculates MP2 1st derivatives (forces),and forms A-matrix and MO integrals for SCF 2nd derivatives.

3–2 Turbomole

Organization of Turbomole Implementation

Impl

emen

tatio

n• TurboNMR calculates NMR shieldings.

• TurboPOLLY calculates electrostatic polarizabilities and 1st hyperpolarizabili-ties.

• TurboPROP calculates 1-electron properties, performs MO localization, performspopulation analyses, and calculates relativistic correction to SCF energy.

• TurboSCF generates converged SCF MOs and calculates SCF energy.

• TurboXCITE calculates frequency-dependent polarizabilities, as well as excited-state transition energies and oscillator strengths.

The various Turbomole C-shell and awk scripts are summarized in the following list:

• add_car_to_arc add current .car file data to .arc file.

• add_car_to_arc.awk add current .car file data to .arc file.

• atom_digest create list of element symbols from .car file.

• build_tmol_basis gets basis set and ECP data from a library.

• build_tmol_basis.awk gets basis set and ECP data from a library.

• cleanup_restart.awk resets the run_name_route.csh file for a restarted job.

• clip_data_group.awk clips an individual data group out of the control file (or basisset library).

• constraint_format.awk reformats constraint input data.

• coord_to_car converts the geometry in an input file to a .car file.

• cvt_tmol_input converts an Turbomole input file to a control file.

• execute_job runs a step of the Turbomole job.

• geom_digest digests geometry from the input file.

• get_atomic_number converts atomic symbol to atomic number and vice versa.

• get_car_elements.awk create list of element symbols from the .car file.

• get_proper_files.awk handles the files from which the starting MOs, starting Hes-sian, and point charges are read.

• lc_first.sed translates the input file to all lower case, except for the last word oneach input line.

• mixup.awk handles mixed basis set input.

• optimize is the driver script for the OPTIMIZE executable.

• qwhich finds the path to an executable or script (It's a modified version of theUNIX which command.).

Turbomole 3–3

Implementation Organization of Turbomole

Implem

entation• reset_convergence.awk resets the $scfconv and $denconv control file data for

optimize + frequency jobs.

• scan_outmol creates a .sum file from the .outmol file.

• scan_outmol.turbomole.awk creates a .sum file from the .outmol file.

• set_stat_flag sets the $statistics flag in the Turbomole control file.

• tickmark.awk keeps track of which steps in a job have been completed.

• tmol_input_to_ctrl.awk converts a Turbomole input file to a control file.

• turbomole is the master Turbomole job script.

Normally, you will have no need to explicitly use any of the individual executables orscripts (other than the turbomole script); however, advanced Turbomole users maywant to use the executables outside of the context of the turbomole script or to modifyone of more of the scripts for performing special tasks.

3–4 Turbomole

Organization of Turbomole Implementation

Impl

emen

tatio

n

Turbomole 4–1

Comm

ands

4 Command Summary—The InsightEnvironment

Turbomole is accessed in the Insight environment by choosing Turbomole from theModule pulldown (that is, click the Biosym logo and select Turbomole from the listthat appears). The Turbomole module contains several pulldowns (in addition to thecore pulldowns on the top menu bar), which appear on the lower menu bar. They are:Setup, Symmetry, Optimize, Background_Job, Run, and Analyze. Each pulldowngives access to several related commands. The Setup pulldown, for example, containsa set of commands used in setting up a Turbomole calculation: System, Parameters,and Setup_Grid_Output.

What the commands in these pulldowns do is summarized briefly below. For moredetailed explanations of individual commands, refer to the Insight program’s on-linehelp facility (by clicking the help icon, which is the button containing a question mark,on the left side of the main Insight window). For information on how to use these com-mands, see Chapter 5, Methodology—The Insight Environment.

Setup Pulldown

The commands accessed with the Setup pulldown are used to set up the Turbomolejob.

The Setup/System command defines the name of the molecule or assembly that youwant to work with and allows you to select the basic type of calculation.

The Setup/Parameters command is used to define all Turbomole parameters for a cal-culation. The predefined default values are appropriate for most calculations. You may,however, need to change specific parameters to refine your calculation. It allows youto:

• Set the calculation method to Hartree–Fock, MP2, DFT, or ACM.

• Define the atomic basis set.

• Decide whether to use effective core potentials.

4–2 Turbomole

Symmetry Pulldown Command Summary—The Insight Environment

Com

man

ds• Control disk usage.

• Define electronic state parameters for your molecule.

• Define parameters for the self-consistent field (SCF) calculation.

• Specify additional properties to be calculated by Turbomole.

• Set parameters that determine what 3D grid data are generated from the SCF wave-function.

The Setup/Setup_Grid_Output command allows you to set up the parameters thatdetermine the boundaries and resolution of the 3D grid used for plotting molecularorbitals, electron density, and molecular electrostatic potentials. Note that this com-mand is not needed if no plotting is selected.

Symmetry Pulldown

The Symmetry/Find_Pt_Group command allows you to determine the point-groupsymmetry and number of degrees of freedom of a molecule or assembly. If a pointgroup is found for the system, the atomic coordinates are symmetrized and the mole-cule is transformed, using symmetry, into the right axis system for calculation.

Optimize Pulldown

The Optimize/Opt_Parameters command is used to define parameters for an optimi-zation job.

The Optimize/Constraints command is used impose atom and geometry constraintson a molecule.

Background_Job Pulldown

The commands accessed with the Background_Job pulldown are used for controllingand monitoring the execution of your Turbomole job.

The Background_Job/Setup_Bkgd_Job command allows you to set up the executionmode and select the host upon which to run a job. This command is also used to controlthe notification method for background job completion and cleanup options.

The Background_Job/Control_Bkgd_Job command allows you to coordinate run-ning background jobs by detaching selected background jobs from or attaching themto the current Insight session. In addition, this command allows you to specify theinterval for invoking a task specific to a particular background job for processing itsoutput.

Turbomole 4–3

Command Summary—The Insight Environment Run Pulldown

Comm

andsThe Background_Job/Completion_Status command allows you to monitor andevaluate the completion status of one or all background jobs. In addition, this com-mand can be used to look up the meaning of a return status code.

The Background_Job/Kill_Bkgd_Job command is used to terminate execution of abackground job that was submitted during the current Insight session.

Run Pulldown

The Run/Run_Turbomole command allows you to assign a name to your job and tostart the calculation. The run name is used to identify the input and output files associ-ated with the job.

Analyze Pulldown

The commands accessed with the Analyze pulldown are used to display and analyzethe results of a completed Turbomole job.

The Analyze/Orbital_Contour command allows you to display both the plus andminus phases of a molecular orbital in one step, at any grid level, and to customize theircolors.

The Analyze/Normal_Mode command is used to create a graph of your molecule’sIR spectrum and to animate the molecule according to its normal modes of vibration.

The Analyze/Density_of_States command is used to do a total or partial density ofstate analysis.

The Analyze/Scan_TMol_Output command allows you to examine the output file fora calculation that is still running or one that has already ended.

4–4 Turbomole

Analyze Pulldown Command Summary—The Insight Environment

Com

man

ds

Turbomole 5–1

Methodology

5 Methodology—TheInsight Environment

This section is a general description of how to use the Turbomole module of theInsight program. On-line help (accessed by clicking the help icon) contains furtherdetails about what individual commands and parameters do. The Insight documenta-tion provides general information on filling in parameter values, executing commands,the various parts of the Insight window, using the mouse, etc.

Commands provided in the Turbomole module are discussed in general terms in theorder in which they are used in a typical calculation. Also included are hints aboutwhen certain parameter values should or should not be used.

Using Turbomole in the Insight Environment

The Turbomole module is used to set up and then start a Turbomole calculation.Unlike many commands in the Insight program, nothing actually happens until theTurbomole job is started, making it possible to set up complex calculations and even(by temporarily leaving the Insight program to use a text editor) edit or change partsof the calculation before the job is started. The command input file that is built upthrough the Insight interface (called run_name.input) is eventually translated into acontrol file which directly controls the Turbomole run (see Appendix C for additionalinformation on files).

The commands in the Turbomole module can be grouped into four classes, roughlycorresponding to the four basic steps of a Turbomole calculation:

• The Setup/System command is used to select the molecule and choose the type ofcalculation. The Symmetry/Find_Pt_Group command is used to find or set thepoint-group symmetry of the molecule.

• The Setup/Parameters, Setup/Setup_Grid_Output commands and the Opti-mize pulldown are used to set up the calculation input parameters and to specifythe desired optional properties to be calculated.

• The Background_Job and Run pulldowns are used to specify run conditions andstart the Turbomole job.

5–2 Turbomole

Outline of Basic Steps of a Turbomole Calculation Methodology—The Insight Environment

Met

hodo

logy

• The Analyze pulldown (and other pulldowns and icons that are part of the Insightinterface) aids in analyzing the results of the calculation.

The relation of these commands to the basic steps of a Turbomole calculation is out-lined in the following section, and a detailed description of how the commands andparameters accessed via these pulldowns are used is presented under Setting up Calcu-lations with the Commands in the Turbomole Module (starting on page 5–3).

Outline of Basic Steps of a Turbomole Calculation

Step 1: Defining the Molecule

A Turbomole calculation can be performed on any molecule or assembly of moleculesthat exists in the Insight space (provided it is not too large). Currently, Turbomole cal-culations are limited to systems containing no more than 400 total atoms or 8000 totalbasis functions (with a maximum of 2000 basis functions per irreducible representa-tion). Note, however, that the Turbomole basis set library does not contain basis setsor effective core potentials for the very heavy elements, namely, atoms Am–Lw. Con-sequently, you need to supply your own basis sets for calculations involving any ofthese heavy elements. Molecules can be read from files with the File/Import or Mol-ecule/Get command, be created with the Builder module, or result from work per-formed with another product such as the Discover program. Note that Turbomole doesnot modify the molecule in any way at this stage. Therefore, any desired modifications,such as adding hydrogens or partial charges to a molecule or adjusting its configura-tion, must be done prior to starting the Turbomole calculation. After selecting Turbo-mole from the Module pulldown (which appears when you click the Biosym logo),you then tell it what system you want to work on and what basic type of calculationyou want to do, by using the Setup/System command.

Next, the Symmetry/Find_Pt_Group command may be executed to determine thepoint-group symmetry of the system and, if desired, to use any symmetry that is foundthroughout the subsequent Turbomole calculation. Roughly symmetrical moleculescan be geometrically adjusted to the exact symmetry required for Turbomole calcula-tions by increasing the value of the Symmetry_Threshold parameter.

Step 2: Setting up the Calculation Parameters

The next step is to set the desired input parameters. The Setup and Optimize pull-downs contain commands that specify these parameters as well as toggles that turn onthe calculation of molecular properties and the generation of grid data for 3D plots.Since all these parameters have default values, you need only set them if you want val-ues other than the defaults. Each time you execute one of these commands, the param-eter values that you enter become the new defaults and are used in all subsequentcalculations in the current Insight session. You need to specify what properties andgrid data you want before you start a run.

Turbomole 5–3

Methodology—The Insight Environment Setting up Calculations with the Commands in the Turbomole Module

Methodology

You can read in parameters that were used in a previous calculation by toggling theLoad_Input parameter in the Setup/System command to on. You should also set theCalculation_Type to the same type of calculation specified in the input file you load,since it will otherwise be overwritten by your new choice.

Step 3: Performing the Turbomole Calculation

After all the input parameters are specified, you are ready to run the Turbomole calcu-lation using the commands in the Background_Job and Run pulldowns.

The Background_Job pulldown is used to set non-default run conditions.

The Run/Run_Turbomole command writes out the necessary input files and specifiesa name that is used as the root name for all output files.

The Run_Turbomole command also creates a shell script file (run_name#.csh) thatactually runs the Turbomole calculation. You can have the Insight program automati-cally submit this job to the background or just write it to disk, so that you can submitit manually later.

Step 4: Analyzing the Results

The run_name.sum file contains the results of your Turbomole calculation. You canview its contents with the Insight file/text viewer or any standard UNIX text reader oreditor. You can also use commands in the Analyze pulldown and in other modules ofthe Insight interface to construct grids and graph various properties.

Setting up Calculations with the Commands in the TurbomoleModule

Beginning a Turbomole Session

To access the Turbomole commands, select Turbomole from the Module pulldown(accessed by clicking the Biosym logo). The set of Turbomole pulldowns then appearson the lower menu bar.

Defining the Molecule and Its Point-Group Symmetry

Specifying the System and Type of Calculation

You use the Setup/System command to tell Turbomole the name of the molecule orassembly on which you want to perform calculations and the basic type of calculationyou want to run.

5–4 Turbomole

Setting up Calculations with the Commands in the Turbomole Module Methodology—The Insight Environment

Met

hodo

logy

To specify the system, enter a name in the Object Name parameter box by picking amolecule or assembly in the display area of the screen, choosing its name from theAssem/Mol Names value-aid, or typing it in the Object Name parameter box.

To choose the type of calculation, set the Calculation_Type parameter to one of these:

• Select Energy to compute the electronic energy of your system.

• Select Gradient to compute energy and a single gradient without optimization.

• Select Optimize to optimize the geometry of your system.

• Select Frequency to compute harmonic frequencies and infrared absorption inten-sities at the specified geometry.

• Select Optimize_Frequency to optimize the geometry before computing the har-monic frequencies and intensities.

If you want to load parameter values from an existing .input file, toggle the Load_Input parameter on and enter the name of the input file in the File Name parameterbox. Note that you also need to set the Calculation_Type to match that in the input file.

Select Execute to execute the command.

Finding and Adjusting the Molecular Point-Group Symmetry

To identify the symmetry of your molecule and, if desired, use any symmetry that isfound throughout the subsequent Turbomole calculation, use the Symmetry/Find_Pt_Group command.

Finding the Point-Group Symmetry without Changing the Molecule’sGeometry. To only report existing symmetry, simply execute the Symmetry/Find_Pt_Group command with its parameters left at their default values (Snap_Symmetry= off, Snap_Orientation = off, Symmetry_Threshold = 0.0005). The point-groupsymmetry of your molecule is reported in the message area near the bottom of theInsight window.

If the reported symmetry of the molecule is not as you expect (e.g., if you use theBuilder module to construct formaldehyde to have C2v symmetry, but the Symmetry/Find_Pt_Group command reports Cs symmetry), it is likely that the molecule, asbuilt, is not exactly symmetric and that the Symmetry_Threshold parameter thereforeneeds to be made larger to increase the tolerance for recognizing symmetry. So, if nec-essary, you can repeatedly execute the Symmetry/Find_Pt_Group command withprogressively larger values of Symmetry_Threshold, until the symmetry you expectis reported. Note, however, that if you need to increase the Symmetry_Thresholdparameter above about 0.5 Å, you should use the Builder tools to manually adjust thegeometry before trying again.

Turbomole 5–5


Methodology

Once you determine the point-group symmetry as expected, you may use the Symme-try/Find_Pt_Group command to enforce exact symmetry and/or to use symmetry inyour subsequent Turbomole calculation.

Imposing Exact Symmetry on the Molecule and Using Symmetry inCalculations. To enable your subsequent Turbomole calculation to make use of thepoint-group symmetry and, if necessary, to adjust the geometry and spatial orientationof you molecule so it is exactly symmetric and to align the symmetry coordinates ofthe molecule properly with respect to Cartesian space, execute the Symmetry/Find_Pt_Group command with both Snap_Symmetry and Snap_Orientation toggled onand with Symmetry_Threshold set to the appropriate value (as determined above).

In general, when you execute this command with the Snap_Orientation parametertoggled on, your molecule is translated and/or rotated in space so that its center of massis at the origin of the Cartesian axis system and (if a point group other than C1 isfound), the axis or plane or center of symmetry is aligned properly with the Cartesianaxis system.

Sometimes, you may not want to reorient you molecule (e.g., calculations in which anoriented external environment is included). In these cases, you would not use the Sym-metry/Find_Pt_Group command, and your Turbomole calculation would be runwithout symmetry.

Technical Notes . You must execute the Symmetry/Find_Pt_Group command inorder to take advantage of any symmetry (other than C1) for Turbomole runs that areset up from the Insight interface.

Toggling the Snap_Symmetry parameter on means to attempt to change the relation-ship of the atoms to their ideal symmetry positions (the symmetry is adjusted when thecommand is executed). The symmetry label is displayed whether Snap_Symmetry ison or off. Toggling Snap_Symmetry to on also gives you access to the Snap_Orien-tation parameter.

Snap_Orientation can be toggled only if Snap_Symmetry is on. Toggling the Snap_Orientation parameter on means to attempt to place the molecule in the standard ori-entation around the origin and symmetry axes. Note: this may significantly displaceyour molecule. If Snap_Orientation is off, the molecule orientation does not change.

If you want to execute the Symmetry/Find_Pt_Group command with Snap_Orien-tation toggled on, you must do so before using the Grid pulldown (or icon), to preventa mismatch between the positions of the molecule and the grid.

If the Symmetry/Find_Pt_Group command is not executed with Snap_Symmetryand Snap_Orientation toggled on, C1 symmetry is used in an optimization calcula-tion (even if the Use_Symmetry parameter in the Optimize/Opt_Parameters commandis toggled on).

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Specifying Parameters that Control the Calculation

Using the Setup/Parameters Command

The Setup/Parameters parameter block contains many parameters that allow you tocontrol the details of the Turbomole calculation. (Each time you execute the Setup/Parameters command, the parameter values that you enter become the new defaultsand are used in all subsequent calculations in the current Insight session.) Each ofthese groups of parameters is discussed separately below.

Selecting the Calculation Method

Methods Available. You can use one of the following ab initio methods for Turbo-mole calculations (see Chapter 2, Theory, for details):

Hartree–FockMP2DFTACM

by choosing the appropriate parameter value under the Methods parameter in theSetup/Parameters command.

If you choose DFT, you must also select from among several density functionals. Thiscan be done in two different ways:

1. With the Other_Functionals parameter toggled off (default), you can select one offour standard, predefined density functionals (VWN, BVWN, BPW, and BLYP)from the Functionals parameter list:

2. For greater flexibility, you can toggle the Other_Functionals parameter on, whichallows you to select the individual local and gradient-corrected exchange and cor-relation terms in the density functional using the Local_Correlation, GC_Exchange, and GC_Correlation parameters.

Table 5–1. Standard Functionals Available within the Insight Interfaceof Turbomole

Functionals local correlation GC exchange GC correlation

VWN Vosko–Wilk–Nusair — —BVWN Vosko–Wilk–Nusair Becke-88 —BPW Perdew–Wang Becke-88 Perdew–Wang 91BLYP Lee–Yang–Parr Becke-88 Lee–Yang–Parr

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Methodology

The Local_Correlation parameter is used to select the local correlation functional.The choices for Local_Correlation are:

VWN: (default) The Vosko–Wilk–Nusair parameterization of Ceperley andAlder’s electron gas Monte Carlo data.

None: No local correlation functional.

The GC_Exchange parameter allows you to select a gradient-corrected exchangeterm. The choices for GC_Exchange are:

B_88: Becke’s 1988 version of a gradient-corrected exchange functional.

None: (default) No gradient-corrected exchange term.

The GC_Correlation parameter allows you to select a gradient-corrected correla-tion term. The choices for GC_Correlation are:

LYP: The Lee–Yang–Parr correlation functional, which includes both local andgradient-corrected terms.

PW: The Perdew–Wang 91 correlation functional, which includes both localand gradient-corrected terms.

None: (default) No gradient-corrected correlation term.

If you choose the ACM method, the ACM coefficients are defaulted to Becke’s sug-gested values (Becke 1993). However, they can be adjusted using the Slater_X,VWN_C, B88_X, and PW_C parameters.

Choosing which Method To Use. From a practical point of view in selecting themethod, you need to consider (1) the computational cost, (2) disk and memory require-ments, and (3) the accuracy of the available methods for your particular system.

The relative computational cost of the methods as implemented in Turbomole is:

Hartree–Fock < DFT(VWN) < DFT(BVWN) < DFT(BPW,BLYP),ACM << MP2

For all but small molecules, the Hartree–Fock (HF), DFT, and ACM methods are com-parable in computational cost (all are dominated by the calculation of 2-electron inte-grals, which scales formally as N 4, where N is the size of the system). MP2, however,is an inherently more expensive method (it scales formally as N 5 ).

The disk space requirements of calculations using any of the Turbomole methods canbe tailored to your hardware limitations (see Controlling Disk and Memory Usage,page 5–13). There is, however, a distinction between HF/DFT/ACM and MP2.Whereas for the HF, DFT, and ACM methods, you can request that the calculation berun fully-direct (no disk space be used for storage of 2-electron integrals); with theMP2 method, a minimum amount of disk space is needed (below which the MP2 cal-culation cannot be run—see Controlling Disk and Memory Usage, page 5–13).

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Regarding the accuracy of the ab initio methods in Turbomole, since all the methodsare approximations to the exact solution of the time-independent, electronicSchrödinger equation (see Chapter 2), it is, in general, not possible to know, a priori,which method (when coupled with which basis set, see Selecting the Basis Set, page5–8) will yield the most accurate results for a particular molecular system. Basedpurely on theoretical grounds, the ACM, DFT, and MP2 methods as a group are moreaccurate (they are less severe approximations of the Schrödinger equation) than Har-tree–Fock, in that ACM, DFT, and MP2 include an approximate treatment of electroncorrelation (and Hartree–Fock includes no electron correlation). Of more relevance,however, is the accuracy of the methods and basis sets in applications to a wide varietyof molecular systems. In this regard, recent work by researchers at Biosym/MSI (And-zelm et al. in press) for predictions of energies of a wide variety of reactions involvingmolecules composed of 1st- and 2nd-row elements (hydrogen–chlorine), found theperformance of the methods (from most to least accurate) to be:

ACM > BPW > BLYP > MP2 >> VWN >> Hartree–Fock

For predictions of geometries the relative performance is:

ACM > MP2 > BPW,VWN > BLYP, HF

These conclusions are based on the performance of these methods on average, whichis not necessarily the same as for a particular molecule.

For molecules containing heavier elements, the amount of data available is less abun-dant. However, calculations on organometallic systems and other molecules contain-ing transition metals seem to indicate that the ACM and DFT methods are preferableto HF and MP2.

Selecting the Basis Set

The Basis_Source, Basis_Set_Data, ECP, and ECP_Range parameters allow you toselect the atomic basis functions that Turbomole uses in the expansion of the molecularorbitals. They also enable you to replace core electrons by effective core potentials inyour electronic structure calculation.

The reliability of your results depends critically on selection of an appropriate basisset. While there are no universal laws regarding basis set selection, some rules ofthumb can provide general guidelines. First, you should consider the atom types andnature of the interactions in your molecule. Atoms and bonds that are relatively polar-izable require polarization functions to adequately describe the molecular electrondeformations, while a proper description of weak molecular interactions requires awell saturated basis set to reduce the effects of basis set superposition errors. Youshould also consider the type of information you want from the Turbomole run. Forexample, most molecular geometries and harmonic vibrational frequencies can be reli-ably predicted with small- to medium-sized basis sets (i.e., the Pople basis sets, DZ,and DZ+P); however, reliable predictions of electrostatic moments, polarizabilities,infrared absorption intensities, and excitation energies generally require additional sets

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Methodology

of polarization functions and/or diffuse orbitals. For predicting NMR shieldings, thequality of the basis set near the nuclei is critical; therefore, it is often important (espe-cially for 2nd-row atoms) to use basis sets of TZ quality for describing the s and porbitals. In addition, for MP2 calculations, the character and size of the virtual (unoc-cupied) orbital space becomes important. The virtual orbitals are also constructed fromyour atomic basis functions, and therefore, your choice of basis set plays an additional,indirect role in the quality of MP2 results. Thus, you should use a medium to largebasis set when comparing relative MP2 energies, to allow for a well balanced correla-tion treatment among the molecules being compared.

The Basis_Source parameter allows you to select between reading the atomic basis setdata and, if desired, effective core potential data from Turbomole’s standard basis setlibrary or from some other file.

Using the Basis Set Library. With Library as the Basis_Source, a scrollable list ofstandard basis set choices is provided under the Basis_Set_Data parameter. For moredetailed information than is included in this section, you can refer to the appropriateliterature references cited below or directly to the Turbomole basis set library files,which can be found in $BIOSYM/data/turbomole/bases/

If you select Library as the Basis_Source, your choice of one of the standard atomicbasis sets from the Basis_Set_Data parameter list is read from the Turbomole basisset library and assigned to each of the atoms in your molecule. If you also toggle theECP parameter on, effective core potentials (ECPs) and their associated valence basissets (ECP basis sets) are assigned to all atoms in your molecule which fall within therange specified by the ECP_Range parameter instead of the basis set selected in theBasis_Set_Data parameter list. The basis set assignments for atoms outside theselected range are not affected. For example, for the molecule SbFBr2 with the follow-ing values specified for the basis set and ECP parameters:

Basis_Set_Data dzpECP onECP_Range K-Pu

the Sb and Br atoms would be assigned ECPs and the appropriate valence basis sets,since both Sb and Br fall within the range K–Pu (in the periodic table), but the F atomwould be treated as an “all-electron” atom (since it lies outside the range K–Pu) andbe assigned the DZP basis set.

With Library as the Basis_Source, the standard basis set choices available from theBasis_Set_Data list are:

1. sv

Split-valence (valence double-zeta) basis set for H–Kr (Schäfer et al. 1992).

2. svp

sv basis set plus one set of polarization functions per atom.

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3. dz

Double-zeta basis set for H–Kr (Schäfer et al. 1992).

4. dzp

dz basis set plus one set of polarization functions per atom.

5. tz

Triple-zeta basis set for H–Ar (Schäfer et al. 1992).

6. tzp

tz basis set plus one set of polarization functions per atom.

7. tz2p

tz basis set plus two sets of polarization functions per atom.

8. sto-3g

Minimum STO-3G basis sets for H–Xe (Hehre et al. 1986 and references therein).

9. 3-21g

Split-valence 3-21G basis sets for H–Ar (Hehre et al. 1986 and references therein).

10.6-31g

Split-valence 6-31G basis sets for H–Ar (Hehre et al. 1986 and references therein).

11. 6-31g*

The 6-31G basis sets plus one set of polarization functions on Li–Ar; the 6-31Gbasis set on H and He.

12.6-31g**

The 6-31G basis sets plus one set of polarization functions on H–Ar.

13.dzvd

Valence double-zeta basis set for H–Xe plus one set of polarization functions on allatoms but H and He (Godbout et al. 1992).

14.dzvp

Valence double-zeta basis set for H–Xe plus one set of polarization functions on allatoms (Godbout et al. 1992).

15.tzvp

Valence triple-zeta basis set for atoms H, B–F, Al–Ar plus one set of polarizationfunctions on all atoms (Godbout et al. 1992).

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Methodology

16.cc-pvdz

Correlation-consistent valence double-zeta basis set for H, He, B–F (Dunning1989).

17.aug-cc-pvdz

cc-pvdz basis set augmented with diffuse functions (Kendall et al. 1992).

18.cc-pvtz

Correlation-consistent valence triple-zeta basis set for H, He, B–F (Dunning 1989).

19.aug-cc-pvtz

cc-pvtz basis set augmented with diffuse functions (Kendall et al. 1992).

20.unc-aug-cc-pvtz

aug-cc-pvtz basis set with the s and p shells completely uncontracted.

With Library as the Basis_Source and ECP toggled on, the averaged relativisticeffective core potentials (AREP) and ECP valence basis sets are assigned to the appro-priate in your molecule.

The ECPs provided in Turbomole are the averaged relativistic effective potentials(AREPs) developed by Christiansen et al. and are summarized in Table 5–2. Fordetailed specifications of the AREPs, please refer to the literature references citedbelow the table and/or to the basis set library files located in $BIOSYM/data/turbo-mole/bases/

Table 5–2. Averaged Relativistic Effective Core Potentials and ECP Valence Basis Setsfor Atoms K–Pu

atom core electrons ECPa valence basis set

Li–Ne 1s2 P 4s4p/2s(3,1)2p(3,1)Na, Mg 1s2 P 6s4p/4s(3,1,1,1)2p(3,1)Al–Ar 1s22s22p6 P 4s4p/2s(3,1)2p(3,1)K, Ca 1s22s22p6 H 5s4p/4s(2,1,1,1)2p(3,1)Sc–Zn 1s22s22p6 H 7s6p6d/5s(3,1,1,1,1)3p(4,1,1)3d(4,1,1)Ga–Kr 1s22s22p63s23p63d10 H 3s3p/2s(2,1)2p(2,1)Rb, Sr 1s22s22p63s23p63d10 L 5s5p/4s(2,1,1,1)3p(3,1,1)Y–Cd 1s22s22p63s23p63d10 L 5s5p4d/4s(2,1,1,1)3p(3,1,1)3d(2,1,1)In–Xe 1s22s22p63s23p64s23d104p64d10 L 3s3p/2s(2,1)2p(2,1)Cs–La 1s22s22p63s23p64s23d104p64d10 R 5s5p4d/4s(2,1,1,1)3p(3,1,1)3d(2,1,1)Ce–Lu 1s22s22p63s23p64s23d104p64d10 C 6s6p3d7f/4s(3,1,1,1)4p(3,1,1,1)2d(2,1)2f(6,1)Hf–Hg 1s22s22p63s23p64s23d104p64d104f14 R 5s5p4d/4s(2,1,1,1)3p(3,1,1)3d(2,1,1)

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Using Effective Core Potentials. For systems that include one or more heavyatoms (atoms heavier than Xe) or for large systems, for which including all the elec-trons in the Turbomole calculation would not be practical, it is usually advisable toreplace the core electrons (electrons which are low lying in energy and typically do notplay any role in the chemistry and bonding in molecules) with effective core potentials(ECPs). In addition to reducing the size of the Turbomole calculation, ECPs can par-tially account for relativistic effects (which would otherwise be completely neglectedby Turbomole), which become significant for the core electrons of the heavy elements.However, because calculation of NMR shielding tensors depends critically on thebehavior of the wavefunction at the nuclei, ECPs should not be used for calculationsin which NMR_Shielding is toggled on.

With Library as the Basis_Source, toggle the ECP parameter on to use effective corepotentials in your calculation. ECPs and their associated valence basis sets areassigned to the appropriate atoms in your molecule, based on your choice for the ECP_Range parameter (which becomes accessible in the Setup/Parameters parameterblock when ECP is toggled on).

With the ECP_Range parameter, you select a range of the periodic table (Li-Pu, Na-Pu, K-Pu, or Rb-Pu). All atoms in your molecule that fall within the selected rangeare assigned ECPs (and associated valence basis sets). All atoms that fall outside theselected range are treated as “all-electron” atoms and are assigned the basis set chosenfrom the Basis_Set_Data list.

Reading Basis Sets and ECPs from a User-Supplied File. If you prefer to usebasis sets or ECPs other than those in the Turbomole library, select Read_From_Filefor the Bais_Source parameter. You provide the name of the file from which to readyour own basis set data in the Basis_File parameter box (which becomes accessiblewhen Basis_Source is set to Read_From_File). When the Basis_File parameter boxis in focus (pick the parameter box with your left mouse button), a Turbomole_Filesvalue-aid appears, which provides a scrollable list of all of the .turbo_archive files inyour current working directory. You can select one of the .turbo_archive files in thevalue-aid or type in the name of another file from which to read your basis set (andECP, if present) data.

aECPs are from P: Pacios and Christiansen (1985), C: Cundari and Stevens (1993), E: Ermler et al. (1991),H: Hurley et al. (1986), L: LaJohn et al. (1987), and R: Ross et al. (1990).

Tl–Rn 1s22s22p63s23p64s23d104p65s24d105p64f145d10 R 3s3p/2s(21)2p(21)Fr–Ra 1s22s22p63s23p64s23d104p65s24d105p64f145d10 E 5s5p4d/4s(2,1,1,1)3p(3,1,1)3d(2,1,1)Ac–Pu 1s22s22p63s23p64s23d104p65s24d105p64f145d10 E 5s5p4d4f/4s(2,1,1,1)3p(3,1,1)ed(2,1,1)3f(2,1,1)

Table 5–2. Averaged Relativistic Effective Core Potentials and ECP Valence Basis Setsfor Atoms K–Pu

atom core electrons ECPa valence basis set

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Methodology

Your basis set file must include at least one basis set for each atom type in your mole-cule (it may contain more than one basis set entry for a particular atom type; however,only the first such entry is used—the remainder are ignored). Any ECPs appearing inyour basis set file are applied to all atoms of the particular atom type(s) for which theECP entry(ies) appear (i.e., you do not need to toggle on the ECP parameter or selecta range using the ECP_Range parameter).

The basis set (and, if desired, ECP) data must appear in Turbomole control file format.Refer to the Basis keyword (page E–10) for specifications of the format for basis setand ECP entries in your basis set file.

One technical point to note on basis function usage: while the standalone mode of run-ning Turbomole does provide an input file keyword for switching between the true5d7f and the Cartesian 6d10f orbital representations (see Basis_Type keyword, pageE–25), the Turbomole module in the Insight program does not provide access to thiskeyword. Consequently, unless you modify your input file by hand before launchingyour job, the following rule applies:

Controlling Disk and Memory Usage

During each iteration of the SCF procedure, two-electron integrals of the form:

Eq. 5–1

are needed. In Eq. 5–1, the one-electron functions φ (r) are the atomic basis functions,with each of the indices µ, ν, λ, σ spanning the basis set. Thus, the total number of two-electron integrals (neglecting symmetry and integral cutoffs) is proportional to N4,where N is the number of atomic basis functions. Since the integrals are independentof the SCF MO coefficients, the traditional SCF method involves a one-time precalcu-lation and disk storage of all of these AO integrals. They are subsequently read fromdisk as required during each SCF iteration. Such an approach often creates a disk I/Obottleneck and limits the size of your molecular system to one for which all the AOtwo-electron integrals can fit on your available disk space.

The newer “direct” and “semi-direct” SCF schemes used in Turbomole eliminate thisdisk space limitation by providing the flexibility to store only a portion (semi-directSCF) or none (direct SCF) of the AO two-electron integrals on disk. All integrals notstored on disk are recalculated each time they are needed. Similarly, for calculations in

basis set representation

3-21G, 6-31G, 6-31G*, 6-31G** 6d10fall other basis sets

(including those read from a user-supplied file)5d7f

µν λσ( ) r1 r2d φµ*

r1( ) φν r1( ) r1 r2– 1– φλ*

r2( ) φσ r2( )d∫=

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which two-electron integrals (and other two-electron quantities) are needed in themolecular orbital basis (SCF frequency calculations and all MP2 calculations), Turbo-mole uses semi-direct algorithms for the calculation and disk storage of these MO two-electron quantities as well.

The AO_Ints and MO_Ints parameters are used to specify the amount of disk space(in MBytes) that you want to use for storing AO two-electron integrals and MO two-electron quantities, respectively (the MO_Ints parameter appears in the Setup/Parameters parameter block only when Methods = MP2 or Calculation_Type (inthe Setup/System command) = Frequency or Optimize_Frequency). For AO inte-gral storage, you can specify that no disk space be used (AO_Ints = 0) to run a directSCF calculation, although it is more efficient (in terms of SCF CPU time) to run asemi-direct SCF computation (AO_Ints > 0). For MO integral storage, there is a min-imum amount of disk storage that is necessary for any given SCF frequency or MP2calculation, below which the calculation cannot be run with Turbomole (the minimumamount is not a fixed quantity but is a function of the size of the molecule, the size ofthe basis set, the symmetry of the molecule, etc.). If the value you specify for MO_Intsis below the minimum necessary to run the calculation, your job will abort with a mes-sage indicating what the minimum MO integral disk storage requirement is. Like forAO integral storage, the more disk space you can provide for MO integral storage, themore CPU-efficient your calculation will be.

For SCF frequency and MP2 calculations, you can also specify the amount of in-corememory to use for holding the A-matrix during the solution of the coupled-perturbedHartree–Fock (CPHF) equation (see Chapter 2, Theory). The amount of memory (inMBytes) is specified using the Max_Core parameter, and, like for disk storage, themore memory you can provide, the more CPU-efficient your calculation will be (if youprovide a value for Max_Core that exceeds the actual physical memory capacity ofyour computer, you will greatly reduce the efficiency of your job, since large amountsof memory paging will occur).

Defining the Electronic State

The Spin, Charge, and Mult parameters are used to define the electronic state of yourmolecule. Based on your specifications for these parameters, Turbomole determinesthe orbital occupations and spin-pairings automatically.

The Charge parameter is used to define the total molecular charge (and thus the totalnumber of electrons to be included in your calculation). The default value of 0 is appro-priate for neutral molecules. If your system is a cation or anion, you would specify apositive or negative integer value, respectively.

If you want to carry out a calculation on the ground electronic state of a closed-shellsystem (all electrons spin-paired), the Restricted (default) selection of the Spinparameter automatically establishes a closed-shell electronic state in which a (neces-sarily) even number of electrons (2n) are paired off into the n lowest-energy molecularorbitals (determined by an extended Hückel calculation). With Spin = Restricted, the

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Methodology

Mult parameter does not appear in the Setup/Parameters parameter block, since theelectronic spin multiplicity is, by definition, equal to 1.

If you want to carry out a calculation on an open-shell electronic state of your mole-cule, you need to set Spin to Restricted_Open or Unrestricted and to specify theelectronic spin multiplicity in the Mult parameter box. Turbomole automaticallyestablishes the lowest-energy open-shell electronic state (based on the results of anextended Hückel calculation) consistent with the charge and spin multiplicity. SettingSpin = Restricted_Open establishes an open-shell SCF wavefunction in which each“closed-shell” orbital (i.e., each orbital that is fully occupied) is restricted to be spa-tially identical for spin-up (alpha) and spin-down (beta) electrons. Choosing Spin =Unrestricted establishes an open-shell SCF wavefunction in which two spatially dis-tinct sets of molecular orbitals are used: “alpha” orbitals for spin-up electrons and“beta” orbitals for spin-down electrons.

The spin multiplicity is specified using the Mult parameter: values of 1, 2, 3, … resultin open-shell singlets, doublets, triplets, … , respectively. A spin-restricted open-shellwavefunction is a proper eigenfunction of the total spin operator (S2). Conversely, aspin-unrestricted wavefunction can be more flexible (e.g., for studying bond-breakingprocesses); however, it is not an eigenfunction of S2 and, consequently, may sufferfrom contamination from states of higher spin multiplicity.

You may encounter situations where symmetry-dictated orbital degeneracy preventsTurbomole from establishing a unique electronic state based on your Spin, Charge,and Mult parameter specifications. If this happens, your Turbomole job aborts with amessage indicating the nature of the problem. You will have to either provide theorbital occupations and spin pairings explicitly using the interactive Hückel tooldescribed below (set MO_Guess to Interactive_Huckel) or run the calculation with-out symmetry to break the symmetry-enforced orbital degeneracies.

Setting up the SCF Portion of a Turbomole Job

By default, Turbomole uses an extended Hückel (EHT) calculation to generate startingorbitals and orbital occupations for the SCF portion of your job (MO_Guess =Huckel).

If, before running your job, you want to look at the EHT orbital energy diagram andperhaps modify the default orbital occupations and spin-pairings, you can set MO_Guess = Interactive_Huckel and select Execute. This launches a preliminary EHTcalculation which, upon completion, displays an EHT orbital energy diagram (showingthe default orbital occupations) in a new window called MO_DIAGRAM (Figure 5–1).

To utilize symmetry in the interactive Hückel calculation (and thus have the resultantorbital diagram include orbital symmetry), execute the Symmetry/Find_Pt_Groupcommand (page 5–3) before launching the interactive Hückel job.

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Figure 5–1. Window that Shows Results of Interactive Hückel Calculation

An interactive Hückel calculation was run on benzene with Spin set to Restricted andCharge set to 0.

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Methodology

The resulting diagram shows the EHT orbitals ordered by energy (starting with thelowest-energy orbital at the bottom of the diagram and proceeding to higher-energyorbitals towards the top of the diagram). The left-most column contains the MO labels(numerical index + symmetry label), the right-most column contains the orbital ener-gies (in Hartrees), and the orbital occupations are displayed in the middle of the dia-gram where a red box containing an i indicates a spin-up (alpha) occupied orbital, agreen box containing an ! indicates a spin-down (beta) occupied orbital, and a yellowbox indicates an empty orbital. A key to the diagram is provided at the bottom of thewindow. It illustrates the color scheme and displays the current values of the total spinmultiplicity, the total number of electrons, and the total molecular charge.

To remove electron(s) from an orbital, simply click the occupied orbital with the leftmouse button. If Closed_Shell is selected (from the menu bar at the bottom of theMO_DIAGRAM window, see below), both electrons are removed from the orbital. Ifin addition the closed-shell orbital is formally degenerate, all electrons in the degener-ate set are removed with a single mouse click. If Open_Shell or Unrestricted isselected (from the menu bar at the bottom of the MO_DIAGRAM window, see below),the spin-up and spin-down electrons can be removed independently. The Multiplicity,Electrons, and Total Charge display at the bottom of the diagram are updated when-ever electrons are added or removed.

To add electron(s) to an orbital, simply click the empty orbital with the left mouse but-ton. If Closed_Shell is selected (from the menu bar at the bottom of the MO_DIA-GRAM window, see below), both a spin-up and spin-down electron are added to theorbital. If in addition the orbital is formally degenerate, all members of the degenerateset are filled with a single mouse click. If Open_Shell or Unrestricted is selected(from the menu bar at the bottom of the MO_DIAGRAM window, see below), thespin-up and spin-down electrons can be added independently. To add a spin-up elec-tron, use the left box of an empty orbital; to add spin-down electrons, use the right box.The Multiplicity, Electrons, and Total Charge display at the bottom of the diagramare updated whenever electrons are added or removed.

If the default EHT occupations are for a restricted closed-shell wavefunction and youwant to unpair electrons, you should toggle the Closed_Shell/Open_Shell/Unre-stricted button on the menu bar at the bottom of the MO_DIAGRAM window toOpen_Shell (for restricted open-shell spin wavefunctions) or Unrestricted (for unre-stricted spin wavefunctions). This allows you to add or remove spin-up and/or spin-down electrons independently rather than as pairs. Conversely, if the default EHTorbital occupations are for an open-shell state and you want to re-occupy the electronsinto a closed-shell occupation scheme, you should put the electrons into a closed-shellconfiguration and then toggle the Closed_Shell/Open_Shell/Unrestricted button toClosed_Shell.

When you have occupied the orbitals as desired, select the Save button on the menubar at the bottom of the MO_DIAGRAM window. The Spin, Charge, and Multparameter boxes of the Setup/Parameters parameter block are updated according toyour orbital occupation scheme.

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At the bottom of the MO_DIAGRAM window, additional functions are containedwithin a menu bar. The menu bar functions are:

Button 1: Help

Currently inactive.

Button 2: Refill

Resets orbital occupation to default aufbau occupation.

Button 3: Closed_Shell/Open_Shell/Unrestricted

Toggles between spin wavefunctions of restricted closed-shell, restricted open-shell, and unrestricted form.

Button 4: Save

Saves current orbital occupations and updates the Spin, Charge, Mult, and MO_Guess parameters in the Setup/Parameters parameter block according to theoccupations in the diagram and the setting of Button 3. Upon executing the Savefunction, the MO_Guess parameter is automatically set to Read_MOs_From_File (see below) with MO_File set to ia_huckel.turbo_archive. (The ia_huckel.turbo_archive contains the orbitals from the EHT calculation and the orbitaloccupations from the MO_DIAGRAM window.)

Button 5: Exit

Closes and deletes the MO_DIAGRAM window. (This does not save occupationsor set the parameters as does the Save function.)

If you want to start the SCF procedure with a set of MOs from a previous Turbomolecalculation (MOs stored in a .turbo_archive file), set the MO_Guess parameter toRead_MOs_From_File and enter the name of the .turbo_archive in the MO_Fileparameter box, which appears when MO_Guess is set to Read_MOs_From_File.When the MO_File parameter box is active, a list of .turbo_archive files residing inyour current working directory appears, from which you can choose the desired file.To use MOs from a previous Turbomole calculation as starting orbitals for your currentTurbomole calculation, the molecule and molecular symmetry used in the previouscalculation must be the same as those in your current calculation.

The SCF_Conv parameter sets the SCF convergence criteria. The criteria consist oftwo tests, each of which must be satisfied for SCF convergence to be reached.

• Criterion 1: Two consecutive SCF energies (i.e., the total molecular energies fromtwo consecutive SCF iterations) differ by less than 10 exp (SCF_Conv).

• Criterion 2: The norm of the difference density matrix is less than 10 exp (SCF_Conv + 2).

Turbomole 5–19


Methodology

The Iteration parameter sets the upper limit for SCF iterations. If the SCF conver-gence criteria have not been satisfied after Iteration of SCF cycles, the SCF procedureis terminated.

Calculating Other Properties with Turbomole

You can specify additional molecular properties to be calculated. Not all properties areavailable for all possible selections of the Methods and Spin parameters. Therefore,only those properties available for your particular choice of Methods and Spin areaccessible in the Setup/Parameters parameter block.

Toggling the Boys_Localization parameter on allows you to carry out a localizationof the canonical SCF molecular orbitals based on the method of Boys (1960). WhenBoys_Localization is toggled on, the Local_HOMO and Local_Other_MO param-eters appear (under the Volumetric heading). These are used to create plot data for dis-playing any localized occupied orbital.

Toggling the Relativistic_E parameter on allows you to calculate a relativistic correc-tion to the SCF energy based on the method of Cowan and Griffin (1976).

Toggling the Electric_Moments parameter on allows you to calculate the electrostaticcharge, dipole moment, and the second, third, and fourth molecular electrostaticmoments from the SCF wavefunction.

Toggling the NMR_Shielding parameter on allows you to calculate chemical shield-ing tensors for all atoms in your system.

To calculate excitation energies and oscillator strengths for electronic excitations (e.g.,to predict the UV/visible spectrum of your molecule), toggle the Excitation_Energiesparameter on. To specify the details of the excitation energies calculation, you alsoneed to specify values for the Exc_State_Method, State_Sym, Exc_State_Spin, andNumStates parameters.

With the Exc_State_Method parameter, you can choose between an excited-state cal-culation using the singles CI method (Exc_State_Method set to SCI) or random phaseapproximation method (Exc_State_Method set to RPA). The SCI method is lessexpensive, but the RPA method is, in general, more accurate.

With the State_Sym parameter, you specify the symmetry of the excited state(s). Youcan enter the string default, which specifies that excited states which transformaccording to the totally symmetric irreducible representation (e.g., excited states of A1symmetry for a molecule having C2v symmetry) will be calculated. Alternatively, youcan enter the standard label for the particular irreducible representation (in lower casecharacters) (e.g., b1g).

With the Exc_State_Spin parameter, you specify the multiplicity of the excitedstate(s). You can choose between excited spin singlets (Exc_State_Spin set to Singlet)or excited spin triplets (Exc_State_Spin set to Triplet).

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With the NumStates parameter, you provide an integer, n, specifying how manyexcited states to calculate. Turbomole reports the excitation energies and oscillatorstrengths of the n lowest-energy excited states consistent with your choice of Exc_State_Method and Exc_State_Spin.

The Polarizabilities parameters allow you to calculate the Static and Frequency_Dependent molecular electrostatic polarizability. If Frequency_Dependent is tog-gled on, you must also provide the values for the frequency(ies) (in eV) of the field(s)to use in the calculation of frequency-dependent polarizabilities. Frequency-dependentpolarizabilities are calculated at each frequency listed. You may list no more than tenfrequencies and, if more than one frequency is listed, you must separate the values withwhite space.

Toggling the Mulliken parameter on allows you to carry out a Mulliken populationanalysis of the SCF wavefunction (Mulliken 1955). Toggling the Loewdin parameteron allows you to carry out a Loewdin population analysis of the SCF wavefunction.

Toggling the Roby_Davidson parameter on allows you to carry out a population anal-ysis based on occupation numbers from the method of Roby (1974) and Davidson(1967).

Toggling the ESP_Charges parameter on allows you to calculate atomic chargesbased on a fit to the molecular electrostatic potential.

Volumetric Parameters

If you want to display the resultant MOs, electron density, and/or electrostatic potentialfrom your Turbomole calculation, you can specify this using the parameters listedunder the Volumetric heading.

Set the Charge_Density parameter on to generate plot data to represent the totalcharge density.

Set the Potential parameter on to generate plot data for the electrostatic potential.

Set the HOMO parameter on to generate plot data for the highest occupied molecularorbital. Set the LUMO parameter on to generate plot data for the lowest unoccupiedmolecular orbital. Note that, when selecting HOMO or LUMO, if the orbital selectedis a degenerate orbital, grid data are generated for all members of the degenerate set(and stored in separate files).

Set the Other_MO parameter on so that you can enter numbers, separated by spaces,that specify which molecular orbitals to plot. Toggling Other_MO to on activates theMolecular_Orbitals parameter. Use the Molecular_Orbitals parameter to list theindices of the other molecular orbitals for which to generate grid data. These indicesare specified as integers separated by spaces. For example, an entry of 5 6 8 would gen-erate grid data for the orbital amplitudes of the fifth, sixth, and eighth lowest-energyMOs. Note that, when selecting Other_MO, orbital degeneracies are handled as forHOMO and LUMO (i.e., if you selected an orbital that is a member of a degenerate

Turbomole 5–21


Methodology

set, grid data are generated for all members of the set). Additionally, for purposes ofcounting the orbitals (with the lowest-energy orbital being orbital 1), an n-fold degen-erate set of orbitals is counted as n orbitals (not 1 orbital). Thus, in the orbital situationshown below, selecting Other_MO with Molecular Orbitals set to 5, 6, or 7 or select-ing HOMO would generate the same three grid files for the triply degenerate orbitals5, 6, and 7:

To generate grid data for the display of localized occupied orbitals (available whenBoys_Localization is on, see above), you can toggle on the Local_HOMO and/orLocal_Other_MO parameters. With the Local_HOMO parameter toggled on, griddata are generated for the localized HOMO. With the Local_Other_MO parametertoggled on, you provide integers in the Local_Mol_Orbitals parameter box whichspecify the localized occupied orbitals. The rules for specifying these integers are iden-tical to those for the Molecular_Orbitals parameter (see above).

Using OPTIMIZE in the Insight Environment

The recommended procedure for geometry optimization within the Insight programis:

1. Construct the molecule to be optimized using the Builder or read in the geometryfrom an existing .car file or appropriate database.

2. Specify any desired geometric constraints with the Optimize/Constraints com-mand. This may include distance, angle, or dihedral constraints among any atomsin the system. Dummy atoms can be defined with the Pseudo_Atom pulldown (inthe Builder module) to aid in defining constraints that are awkward or impossibleto define with only real atoms.

3. Minimize the geometry interactively, using one of the molecular mechanics force-fields available as part of the Discover package (the default forcefield is adequatefor most routine organic molecules). It is strongly recommended that you also cal-culate a Hessian matrix at this time. (Starting with even a relatively simple mechan-

1

2

3 4

5 6 7

8 9

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ics Hessian can dramatically reduce the number of cycles required to reachconvergence, especially with Cartesian coordinates.) You should also make surethat the desired constraints are met, as much as possible, before starting the optimi-zation run.

4. Check the mechanics-converged geometry for symmetry using the Symmetry/Find_Pt_Group command. If no symmetry is found and you suspect that yourmolecule ought to have some, increase the symmetry tolerance and try again. Ifsymmetry is still not found, try repeating Step 3 with a tighter gradient-conver-gence criterion.

5. Steps 1–4 can be repeated to build, say, the backbone of a molecule and ensure thatit has the desired symmetry and/or constraints before adding side chains and addi-tional functional groups. (Note, that if you do modify the molecule, you will needto recalculate the Hessian, using the same mechanics forcefield as in Step 3. Do thisby invoking the Discover program again.)

6. When you are satisfied with your molecule’s symmetry and constraints, only thenshould you set the remaining optimization parameters and prepare your job for sub-mission.

The advantages of starting an optimization with a reliable Hessian are clear fromTable 5–3, which shows the number of cycles to reach convergence with various Hes-sian options for a test suite of molecules covering a range of various point-group sym-metries in both Cartesian and natural internal coordinates.

Using a good starting Hessian is virtually mandatory in optimizations in Cartesianspace, which perform very poorly otherwise, especially for larger systems with littleor no symmetry (Table 5–3). Optimizations in natural internal coordinates are muchless sensitive to the initial Hessian data—the (default) diagonal Hessian is, in general,just as good as a full mechanics-generated Hessian. Thus, if you are optimizing in nat-ural internal coordinates, an input Hessian is not obligatory for good performance.

However, under certain circumstances the topology of your molecule might be suchthat OPTIMIZE has difficulty generating a complete set of internal coordinates. If thisoccurs, the default procedure is to switch to Cartesian coordinates, where a startingHessian is needed. Bear this in mind when deciding whether or not to generate a Dis-cover Hessian for your ab initio optimization.

Optimization parameters are set within the Insight environment by selecting the Opti-mize/Opt_Parameters command. When this command is first selected, the parameterblock shown in Figure 5–2 appears (page 5–24). The parameters and their meaningsare discussed below.

Coordinate_System refers to the coordinates used to describe the molecule to be opti-mized. These can be Cartesian or Internal coordinates—the latter are generated auto-matically by OPTIMIZE, so no user input is required. The default is Internal/Cartesian, which means that OPTIMIZE attempts to generate a set of internal coordi-nates and use these, but if this fails, the program switches to Cartesian coordinates.

Turbomole 5–23


Methodology

Table 5–3. Efficiency of Optimization under Various Conditions

Number of optimization cycles needed to reach convergence for minimization using Cartesian and internalcoordinates, starting with a unit, a diagonal, or a molecular mechanics-derived Hessian. Calculations weredone with Turbomole, but the same general results would be obtained in any optimization.

molecule

numberof

atomssymmetry

group

numberof

variables

Cartesian coordinates internal coordinates

unitHessian

mechanicsHessian

unitHessian

diagonalHessian

mechanicsHessian

water 3 C2v 2 5 5 7 5 6ammonia 4 C3v 2 7 6 7 5 6acetylene 4 D*h 2 7 6 5 7 6benzene 12 D6h 2 6 4 5 3 4ethane 8 D3d 3 7 4 6 4 5propadiene 7 D2d 3 10 5 8 5 5neopentane 17 Td 3 10 5 7 5 51,3,5-trifluoro-

benzene12 D3h 4 7 5 6 5 5

hydroxysulfane 4 C1 6 21 11 17 10 8disilyl ether 9 C2v 7 27 10 13 8 8acetone 10 C2v 8 22 7 7 6 6furan 9 C2v 8 10 8 11 7 8naphthalene 18 D2h 9 11 5 9 7 5methylamine 7 Cs 10 10 5 7 5 61,3,5-trisilacyclo-

hexane18 C3v 11 36 8 14 8 8

1,3-difluoroben-zene

12 C2v 11 8 5 9 6 5

ethanol 9 Cs 13 18 6 8 6 6difluoropyrazine 16 C2h 15 21 8 11 9 91,5-difluoronaph-

thalene18 C2h 17 16 6 11 7 6

benzidine 26 D2 18 26 10 25 12 9benzaldehyde 14 Cs 25 17 6 9 6 64-methyl-3-

penten-2-one17 Cs 28 38 7 9 8 7

2-amino-4-pteri-dinol

17 Cs 31 23 9 12 11 10

2-hydroxybi-cyclopentane

14 C1 36 45 15 23 13 15

caffeine 24 Cs 42 39 10 11 10 12histidine 20 C1 54 102 30 44 23 19dimethylpentane 23 C1 63 29 9 15 16 12menthone 29 C1 81 100 14 26 16 13

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Specifying Cartesian or Internal forces the coordinate choice. For successful optimi-zation using Cartesian coordinates, a reliable starting Hessian (read from a file speci-fied by Hessian_File after toggling Starting_Hessian to on) is recommended.

Use_Constraints is toggled on (indicated by highlighting and a pushed-in appear-ance) if you already set any geometric constraints for your molecule with the Opti-mize/Constraints command. Two algorithms are available for constrainedoptimization: Penalty functions and Lagrange multipliers. The former is more robust;the latter is more accurate and more efficient. The Lagrange/Penalty choice meansthat OPTIMIZE first tries the Lagrange multiplier algorithm and, if this fails, it thenswitches to penalty functions. Another option, Penalty/Lagrange, uses penalty func-tions and, at convergence, refines the final structure using Lagrange multipliers. Spec-ifying Penalty or Lagrange forces a particular algorithm.

Figure 5–2. Default Appearance of the Optimize/Opt_ParametersParameter Block

This is the appearance of the Optimize/Opt_Parameters parameter block the first timethis command is selected, if the parameters in the Session/Cmd_Display commandhave not been changed. (Please see the Insight User Guide for information on theeffects of the Session/Cmd_Display command.)

Turbomole 5–25


Methodology

You may have convergence problems if you use angle constraints near 0˚ or 180˚. Itmay be necessary to optimize using only penalty functions first and then use theLagrange multiplier method in a separate run after the first has converged.

The current maximum number of specific distance or angle constraints that is allowedis ten. More “constraints” can be set by freezing atom positions: any number of atomsmay be frozen. You may request other distance and angle constraints and frozen coor-dinates in the same job; however, take care that your constraints are not mutuallyexclusive.

Note that constrained transition-state searches can be done only with the Lagrangemultiplier method—the penalty function algorithm cannot be used.

Use_Symmetry is on if you used the Symmetry/Find_Pt_Group command to findthe symmetry of your molecule.

Locate_Trans_State should be toggled on if you want to optimize to a transition state.The Calc_Mode parameter becomes accessible when Locate_Trans_State is on andis used to indicate which Hessian mode to maximize—the default is to maximize alongthe lowest mode. Other modes can be requested by setting Calc_Mode accordingly;however, this is not recommended unless you know the Hessian structure in somedetail. Note that, without a reasonable starting Hessian, transition-state searches havelimited chances of success.

GDIIS_Mode invokes the GDIIS algorithm of Pulay (Pulay 1982). This is availablefor minimization only. GDIIS calculates the new geometry as a linear combination ofthe current geometry and geometries from previous optimization steps; the total num-ber of such geometries utilized is given by Max_DIIS, which becomes accessiblewhen GDIIS_Mode is set to Manual. A suggested range for Max_DIIS is 2–10. Set-ting GDIIS_Mode to Automatic causes OPTIMIZE to estimate a suitable value forMax_DIIS based on the number of degrees of freedom.

Tolerances refers to the criteria that must be met for the geometry to be consideredconverged. The Gradient criterion and either the Energy_T or Step_T criteria (orboth) must be satisfied for the optimization to be considered converged.

Gradient is the convergence criterion for the maximum component of the gradientvector (in atomic units). The default is 0.0003, which should be more than sufficientfor most purposes. To obtain accurate vibrational frequencies for very floppy mole-cules, this value should be reduced.

Energy_T is the convergence criterion for the energy change from the previous opti-mization step (in atomic units). The default is 0.000001 Hartree.

Step_T is the convergence criterion for the maximum predicted displacement, that is,the maximum component of the displacement vector for the next step (in atomic units).The default is 0.0003, which should be more than sufficient for most purposes. Forvery floppy molecules this value can be increased without affecting the energetics.

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Num_Steps is the maximum number of optimization cycles allowed for the job. Thedefault is 50, which should be more than enough under most circumstances. If conver-gence is not achieved in Num_Steps steps, the job aborts.

Max_Step is the maximum allowed step size, that is, the maximum permitted lengthof the displacement vector from one optimization cycle to the next (in atomic units).The default is 0.3. For awkward optimizations (e.g., to transition states or very shallowminima) with starting geometries known (or suspected) to be close to the final con-verged geometry, Max_Step should be reduced.

All optimizations, especially those using Cartesian coordinates, should be initiatedwith a good starting Hessian. For standard minimizations, a good Hessian can beobtained from the Discover program; for transition-state searches, Turbomole shouldbe instructed to calculate a Hessian before starting the optimization (by selecting theSetup/System command and choosing the Frequency option).

Toggling Hessian_Update to on enables you to access the Hessian_Update_Modeparameter, which indicates the manner in which the starting Hessian is updated duringthe optimization procedure. Three update methods are supported: Powell, BFGS, andBFGS_Safe. Defaults are provided, depending on the settings of various other param-eters in this parameter block. These defaults should not be changed.

The Powell update is a general-purpose method that allows the Hessian eigenvaluestructure to change. It is the default for a transition-state search.

The BFGS update is the standard default method for minimization. This update tendsto preserve positive definiteness, that is, if the Hessian on a particular cycle has all pos-itive eigenvalues, this situation is likely to carry over to the next cycle, hence its suit-ability for minimization.

The BFGS_Safe update is like the normal BFGS, except that additional safeguardsensure that a positive-definite Hessian always remains so. If this property is threatened,Hessian updating is skipped for that cycle. This is the default for an optimization usingGDIIS.

When the parameter block initially appears (Figure 5–2), the default options that areapplicable to an unconstrained minimization using the EF algorithm are highlighted.Indeed, if a standard minimization is all you intend to do, there is no need to select theOptimize/Opt_Parameters command at all. The parameter block expands (orgrayed-out parameters become accessible) when certain options are selected. Forexample, setting GDIIS_Mode to Manual makes the Max_DIIS parameter boxaccessible (see Figure 5–3, page 5–27)), allowing the size of the iterative subspace tobe set (the default is 4).

When you have set all the parameters in this parameter block, select Execute to actu-ally set the internal Turbomole parameters and to exit the parameter block.

Turbomole 5–27


Methodology

Setting up Grid Output

The Setup/Setup_Grid_Output command allows you to set up the parameters thatdetermine the boundaries of the grid for generation of 3D data.

The Grid_Style parameter allows you to select the method used to compute the gridboundaries. Setting Grid_Style to Enclosure automatically determines the upper andlower limits of the x, y, and z dimensions of the grid, based on the coordinates of themolecule and the value of the Border_Space parameter. The value of the Border_Space parameter (in angstroms) is added to the maximum value in each of the x, y, andz dimensions spanned by the molecule, and, similarly, subtracted from the minimumvalue in each dimension to define the 3D rectangular region of the grid.

You also need to specify the method for determining the positions of the grid points.With Grid_Style set to Enclosure, you specify the grid points with the Number_of_

Figure 5–3. Appearance of Optimize/Opt_Parameters Parameter Blockafter GDIIS_Mode is set to Manual

Here, the GDIIS_Mode parameter has been set to Manual, which makes the Max_DIISparameter box available (compare Figure 5–2).

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Steps parameter. The Number_of_Steps parameter allows you to choose the numberof points per dimension of the 3D grid. These points are evenly spaced in each of thex, y, and z dimensions. This method provides a constant number of points in eachdimension, but not a constant point density for any molecule or assembly. Note that thelower boundaries of the grid will be shifted so that the grid points fall exactly on thegrid boundaries.

With Grid_Style set to Extents, you explicitly specify the upper and lower gridboundaries in each of the X, Y, and Z dimensions, using the Lower_Bounds andUpper_Bounds parameters.

With Grid_Style set to Extents, you also need to specify the positions of the gridpoints with the Grid_Step parameter. The Grid_Step parameter allows you to specifythe distance, in angstroms, between points in each dimension of the 3D grid. This valuemust be greater than zero. This method provides a constant density of points in eachdimension of any size grid.

Setting Up the Background Job

Use of the Background_Job pulldown is optional. If it is not used, the default is to runall jobs on the local host in Cont_Insight mode (see the Background_Job/Setup_Bkgd_Job command). If you prefer this mode, you do not need to read the remainderof this subsection.

When the Background_Job/Setup_Bkgd_Job command is used, the background joblist shows only those background jobs that are run from the current module and can berun on a remote host. If the module contains only one job, the parameter is automati-cally filled in. The list of hosts shows only those hosts that are associated with thatbackground job in the background_job_hosts file at your site. It is possible for you tospecify a remote host that is unavailable (off line, for instance) or for which you haveno login account.

Use the Background_Job/Control_Background_Job command to coordinate run-ning background jobs by detaching selected jobs from or attaching them to Insight. Inaddition, you can use this command to specify the interval for invoking a task specificto a particular background job for processing its output.

Every background job submitted via the generic background utility is assigned a jobnumber. This number is displayed in the information area when the job is submitted(e.g., Starting Module background job ... as job 1). You shouldnote the job number when the job is submitted, since it can be used later to check thejob’s completion status, control the job while it is still running, or kill the job.

The Setup_Bkgd_Job command does not actually run the command—it simplyrecords your host, Execution_Mode, and other preferences. The default host is Local.Your selected host and Execution_Mode are used for any subsequent background jobsfor the duration of the Insight session. When you start a new session, all backgroundjob parameters are again set to their default values.

Turbomole 5–29


Methodology

The Execution_Mode parameter allows you to run a background job concurrently(Cont_Insight) or interactively (Wait_For_Job) or to simply create the necessarycommand files to submit the job, but not actually execute them (Cmd_File_Only).

The Send_Mail parameter allows you to have the system send you an electronic mailmessage upon completion of the background job. This parameter is not active ifExecution_Mode is set to Wait_For_Job. You may find this option useful when run-ning long jobs where you exit the Insight program before the job completes.

The Save_Cmd_Files parameter allows you to save the command file used to submitthe background job bkgd_job_run_name#.csh). Otherwise, this file is deleted when thejob completes. This parameter is not active when Execution_Mode is set to Cmd_File_Only.

All background jobs return a completion status. The completion status is an integercode that indicates success, failure, and/or reason for failure of the job. The status codeis displayed when you are notified that the job has completed.

If you consistently want to send background jobs to another host, you can modify yourpersonal Insight startup file to invoke Setup_Bkgd_Job for each module’s back-ground jobs that you want to assign automatically. Note that you must first change tothe module in which the background job’s interface is found before using Setup_Bkgd_Job to set a preference for that background job.

The Completion_Window parameter can be used to prevent the notification windowfrom appearing when the background job completes. The default is on.

Support for the network queuing system (NQS) is now available in the Background_Job/Setup_Bkgd_Job command.

For the user interface to present parameter defaults and a value-aid containing avail-able queues, and to correctly formulate an NQS command, the user’s NQS queue envi-ronment information must be provided to the Insight program. The Background_Job_Hosts file contains the NQS queue information, or you may enter the requiredinformation directly using the Background_Job/Setup_Bkgd_Job command.

Based on the parameter values provided in the Background_Job/Setup_Bkgd_Jobcommand when Submission_Mode is set to Queued, the Insight background jobmechanism formulates a standard NQS command and starts a process to execute it. Itis assumed that the NQS command constructed by the Insight program functions withyour NQS configuration.

Starting the Job

Use the Run/Run_Turbomole command to assign a name to and initiate your Turbo-mole job. The run name is used to identify the input and output files associated withthe job.

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Monitoring a Background Job

The Background_Job/Completion_Status command has three modes of operation.The One_Job option displays a brief message indicating if a specific job has com-pleted. The message is displayed in the information area of the screen. Certain back-ground jobs generate a status file containing additional information while they arerunning. If this additional status information is available, it is displayed in the textport.If All_Jobs is chosen, the job number, job name, run name, status code, and job statusare displayed in the textport for every job submitted during the current Insight session.The Look_Up_Status option is used to look up the meaning of a return status code.

The Report_Mode parameter is used to indicate what information you would like thecommand to return: status of one job, status of all jobs, or the meaning of a return statuscode from a particular job.

The Job_Number parameter becomes active when One_Job is selected. It is used tospecify the background job that you want to monitor.

The Background_Job and Status parameters become active when Look_Up_Statusis chosen. They are used to specify a status code that you want to look up.

The Kill_Bkgd_Job command is used to stop execution of a background job by killingits process and, optionally, deleting its output files. The Job_Number parameter isused to specify which background job to kill. A value-aid containing a list of all cur-rently running background jobs is provided. If the Save_Output parameter is toggledon, then all output files generated by the background job are saved when the job iskilled. The default value of this parameter is off, meaning that all output files aredeleted.

Visual Aids to Analyzing Results

Displaying Orbital Contours

The reactivities of molecules may often be determined in terms of the sizes anddetailed shapes of the molecular orbitals that comprise their valence manifolds (Houtet al. 1983). Inspection of the shapes and symmetries of only the highest occupied andlowest unoccupied molecular orbitals is often sufficient to determine whether or nottwo molecules can react and, if they do react, what the stereochemistry of the productis likely to be (Hout et al. 1983).

You can use the Analyze/Orbital_Contour command to automatically contour boththe plus and minus phases of a molecular orbital in one step (the Grid/Contour com-mand requires two separate steps for contouring the plus and minus phases of anorbital; and the contour levels, contour colors, and contour name root parameters haveno default values.)

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Methodology

The name of the grid is specified with the Scalar Grid Name parameter. A name isgiven to a grid during its creation with the Grid/Get command (the Grid pulldown isaccessed from one of the icons along the side of the main Insight window).

The Contour Name Root parameter specifies the root name to be given to the createdcontour objects. Ordinarily you need not pay attention to this parameter, since a uniquedefault name is derived from the value of Scalar Grid Name parameter.

The Contour Level parameter is used to specify the value of the contour to create. Fororbital amplitude contours, the default value of 0.0800 is usually appropriate.

The colors assigned to the plus and minus phases of the orbital contour are specifiedwith the Plus Contour Color and Minus Contour Color parameters, respectively.The color can be specified as a character string such as red, as an RGB triplet of inte-gers specifying the red, green, and blue contributions, or by choosing a standard or cus-tom-mixed color from a color palette value-aid. Control of color is explained furtherin the Insight User Guide.

Displaying Normal Mode Vibrations

The Analyze/Normal_Mode command creates a graph of normal mode frequenciesand intensities from an .outmol file generated in a frequencies calculation. This com-mand also shows animated normal modes (selected by picking a frequency in thegraph) and allows computation of isotope effects by adjusting atomic masses with theIsotope_Subst parameter.

Displaying Density-of-States Information

The Analyze/Density_of_States command creates a total density-of-states plot bybroadening the eigenvalues in an .outmol or .dos file. Partial density-of-states informa-tion (e.g., contributions by atom, atom type, or function) can be viewed from a .dos file(if present).

Once a converged electron density has been calculated, there are several ways to ana-lyze the results, in particular the wavefunction. A convenient way of displaying themolecular orbital spectrum is by constructing and plotting the density of states. Formolecular systems, this is commonly done by graphing the molecular orbitals as afunction of the MO eigenvalues. The degeneracy of the orbitals is then indicated by theheight of the functions.

Displaying a Summary of Turbomole Output

The Analyze/Scan_Turbomole_Output command creates a short text summary (in afile called run_name.sum) of the Turbomole output. The summary includes a list of themost important keywords, the most recent geometry and gradients, the total and bind-ing energies, and information on the molecular orbitals (including information aboutthe symmetry, if any, and the eigenvalues).

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For frequency calculations, the vibrations are included, and if properties were calcu-lated, both Mulliken and Hirshfeld data, as well as the electrostatic moments, are sum-marized.

The run statistics (the computer and CPU used, total CPU time) are included at the endof the summary file.

Using Other Insight Pulldowns

The Grid pulldown (which is one of the icons along the side of the main Insight win-dow) is used to create and manipulate an energy grid for a molecule. You can createand compute the energy grid, display and undisplay it, and write it to an output file thatis readable by the Contour/Get command. You need to define the parameters in theGrid pulldown commands before plotting a Turbomole calculation. Please see theInsight documentation for further information on using the Grid pulldown.

Turbomole 6–1

Tutorial

6 Tutorial—The InsightEnvironment

This chapter describes lessons on using the Turbomole commands in the Insight envi-ronment.

Pilot Online Tutorials

As of this release, most tutorials are now available on-screen for use with the Pilotinterface. To access the online tutorials for the Turbomole program, click the biplaneor mortarboard icon in the Insight interface.

Then, from the Open Tutorial window, select Turbomole tutorials (in release 95.0) orQuantum Mechanics Tutorials and then Turbomole Tutorials (in release 3.00) andchoose from the list of available lessons:

Lessons 1-2 Introduction to the Turbomole ModuleLesson 3 Transition-State Optimization of AlcoholLesson 4 Transition_State Optimization of Tetrazine

You can access the Open Tutorial window at any time by clicking the Open File buttonin the lower left corner of the Pilot window.

For a more complete description of Pilot and its use, click the on-screen help button inthe Pilot interface or refer to the Insight II User Guide.

Overview of Tutorial Lessons

In Lesson 1: Unconstrained Optimization of Acetone in Cartesian Coordinates, youwill be introduced to the process of setting up and running a Turbomole job via theInsight interface and will perform an unconstrained geometry optimization on ace-tone.

The topics covered in this lesson include:

• Building an acetone molecule.

• Running a short mechanics optimization to preoptimize the geometry.

6–2 Turbomole

Overview of Tutorial Lessons Tutorial—The Insight Environment

Tuto

rial

• Determining the symmetry.

• Specifying the electronic state.

• Selecting the basis set.

• Setting other parameters for a Turbomole run.

• Generating an initial Hessian matrix with the Discover program.

• Setting up an unconstrained geometry optimization in Cartesian space.

• Initiating the Turbomole run and viewing its output.

Lesson 2: Constrained Optimization of Acetone in Cartesian Coordinates is similar tothe first lesson, except that you will set a distance constraint before optimizing thegeometry.

In Lesson 3: Transition-State Optimization of Alcohol and Lesson 4: Transition_StateOptimization of Tetrazine, you will learn to set up and perform transition-state calcu-lations to study chemical reactions.

Turbomole 7–1

Comm

ands

7 Keywords Summary—Standalone Mode

This section contains an alphabetical list of all keywords that may appear in the .inputfile, along with a short description of each and the page number on which the fulldescription can be found. The .input file is documented in Appendix C, Files.

Header Keywords (used for job identification purposes only)

The presence (or absence) of the header keywords has no effect on the Turbomole job.

Product

Identify which Biosym/MSI quantum product is being run. . . . . . . . . page E–68

Title

Provide job title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–76

Version

Identify version of product . . . . . . . . . . . . . . . . . . . . . . . . . page E–76

Primary Job Control Keywords

The primary job control keywords are used to specify the most fundamental aspects ofyour job (i.e., the type of calculation to perform, the method to use, the basis set to use,etc.). Thus, these keywords almost always need to be present in your .input file.

Basis

Select basis set. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–10

Calculate

Select calculation to be run . . . . . . . . . . . . . . . . . . . . . . . . . page E–26

Charge

Specify total molecular charge . . . . . . . . . . . . . . . . . . . . . . . page E–28

7–2 Turbomole

Additional Job Control Keywords Keywords Summary—Standalone Mode

Com

man

dsGeometry

Specify molecular geometry and units . . . . . . . . . . . . . . . . . . . page E–43

Method

Select quantum method . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–57

Multiplicity

Specify total spin multiplicity. . . . . . . . . . . . . . . . . . . . . . . . page E–60

Spin

Select method for treating spin portion of wavefunction . . . . . . . . . . page E–71

Symmetry

Specify molecular symmetry . . . . . . . . . . . . . . . . . . . . . . . . page E–75

Additional Job Control Keywords

AO_Integral_Filesize

Specify the amount of disk space to be used for storing AO 2-electronintegrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–9

Basis_Type

Select representation of d- and f- type basis functions . . . . . . . . . . . page E–25

ECP

Activate use of effective core potentials . . . . . . . . . . . . . . . . . . page E–32

ECP_Range

Select which elements will be assigned effective core potentials . . . . . page E–33

Max_Core_Memory

Specify the amount of in-core memory to be used for holding A-matrixelements during CPHF . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–56

MO_Guess

Specify initial SCF MOs . . . . . . . . . . . . . . . . . . . . . . . . . . page E–58

MO_Integral_Filesize

Specify the amount of disk space to be used for storing MO 2-electronintegrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–58

Turbomole 7–3

Keywords Summary—Standalone Mode DFT-Specific Keywords

Comm

andsStep_Size

Specify the finite difference step-size to take in finite-difference numericalfrequency calculations. . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–72

Swap_Alpha_Orbitals

Modify default alpha orbital occupations for unrestricted spin states . . . page E–73

Swap_Beta_Orbitals

Modify default beta orbital occupations for unrestricted spin states . . . . page E–73

Swap_Orbitals

Modify default orbital occupations . . . . . . . . . . . . . . . . . . . . . page E–74

DFT-Specific Keywords

ACM_Coeffs

Specify ACM coefficients . . . . . . . . . . . . . . . . . . . . . . . . . . .page E–8

Functionals

Select density functionals . . . . . . . . . . . . . . . . . . . . . . . . . . page E–41

Integration_Grid

Specify integration grid . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–53

Keywords for Controlling the External Environment

Electric_Field

Provide x,y,z components of external electrostatic field . . . . . . . . . . page E–34

Point_Charges

Provide external point charges . . . . . . . . . . . . . . . . . . . . . . . page E–66

Keywords Controlling Calculation of Properties

Boys_Localization

Activate Boys MO localization . . . . . . . . . . . . . . . . . . . . . . . page E–26

Electrostatic_Moments

Activate calculation of dipole, 2nd, 3rd, and 4th Cartesian electrostaticmoments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–35

7–4 Turbomole

Keywords Controlling Calculation of Properties Keywords Summary—Standalone Mode

Com

man

dsESP_Charges

Activate calculation of atomic charges . . . . . . . . . . . . . . . . . . . page E–36

Excitation_Energy

Activate calculation of excited-state transition energies and oscillatorstrengths. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–36

Excited_State_Method

Select method of excited-state calculation . . . . . . . . . . . . . . . . . page E–37

Excited_State_Multiplicity

Specify spin multiplicity of excited state(s) . . . . . . . . . . . . . . . . page E–38

Excited_State_Symmetry

Specify spatial symmetry of excited state(s) . . . . . . . . . . . . . . . . page E–38

Freq_Dep_Polarizability

Activate calculation of frequency-dependent polarizability tensor(s) . . . page E–40

Frequencies

Provide frequency(ies) at which to calculate frequency-dependentpolarizability tensor(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–40

Grid

Define 3D rectangular region for plotting . . . . . . . . . . . . . . . . . page E–51

Loewdin_Analysis

Activate calculation of Loewdin population analysis. . . . . . . . . . . . page E–55

Mulliken_Analysis

Activate calculation of Mulliken population analysis . . . . . . . . . . . page E–59

NMR_Shielding

Activate calculation of nuclear magnetic shielding tensors . . . . . . . . page E–60

Number_Of_Excited_States

Specify the number of excited states to calculate. . . . . . . . . . . . . . page E–61

Plot

Activate generation of 3D grid data for subsequent visualizing in Insightinterface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–64

Turbomole 7–5

Keywords Summary—Standalone Mode Keywords for SCF Tolerances and Convergence Control

Comm

andsRelativistic_Correction

Activate calculation of Cowan–Griffin relativistic correction to SCF energy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–68

Roby_Davidson_Analysis

Activate calculation of Roby–Davidson population analysis . . . . . . . . page E–69

Static_Polarizability

Activate calculation of electrostatic polarizability plus firsthyperpolarizability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–72

Keywords for SCF Tolerances and Convergence Control

Damping

Specify SCF damping procedure . . . . . . . . . . . . . . . . . . . . . . page E–30

DIIS

Specify maximum number of SCF iterations to save for DIIS procedure . page E–31

Level_Shift

Specify virtual orbital level shift procedure . . . . . . . . . . . . . . . . . page E–54

SCF_Density_Convergence

Specify SCF density convergence criterion . . . . . . . . . . . . . . . . . page E–69

SCF_Energy_Convergence

Specify SCF energy convergence criterion . . . . . . . . . . . . . . . . . page E–70

SCF_Iterations

Specify maximum number of SCF iterations to carry out . . . . . . . . . page E–70

Keywords for Control of Geometry Optimization

CONSTRAINT

Define distances, angles, dihedral angles to be constrained during geometryoptimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page E–28

Constraint_Method

Select method for handling geometric constraints during optimization . . page E–29

7–6 Turbomole

Keywords for Control of Geometry Optimization Keywords Summary—Standalone Mode

Com

man

dsDisplacement_Convergence

Specify maximum displacement convergence criterion for optimizer . . . page E–32

Locate

Select type of stationary point to which to optimize . . . . . . . . . . . . page E–55

FIXED

Define Cartesian coordinates to fix during geometry optimization . . . . . page E–39

GDIIS

Activate GDIIS during optimization . . . . . . . . . . . . . . . . . . . . page E–42

Gradient_Convergence

Specify maximum gradient convergence criterion for optimizer . . . . . . page E–50

Hessian_File

Specify initial Hessian matrix for optimizer . . . . . . . . . . . . . . . . page E–52

Hessian_Update

Select Hessian matrix update method for optimizer . . . . . . . . . . . . page E–52

Max_Displacement

Specify maximum step size for optimizer . . . . . . . . . . . . . . . . . page E–56

Opt_Coordinate_System

Select type of coordinate system in which to optimize . . . . . . . . . . . page E–61

Opt_Cycles

Specify maximum number of optimization cycles to carry out. . . . . . . page E–62

Opt_Energy_Convergence

Specify energy convergence criterion for optimizer . . . . . . . . . . . . page E–62

Opt_Use_Symmetry

Activate symmetry use during geometry optimization . . . . . . . . . . . page E–63

Turbomole 8–1

Methodology

8 Methodology—Standalone Mode

This chapter outlines how to run Turbomole in standalone mode. The structure andinterrelationships of Turbomole and its constituent programs is included in Chapter 3,Implementation. The input file structure is documented in Appendix C, Files. Key-words and options are fully described in Appendix E, Commands—Standalone Modeand summarized according to function in Chapter 7, Keywords Summary—StandaloneMode.

Summary

Running a Turbomole Job

Turbomole is run as a standalone software package by executing the following com-mand at the UNIX prompt:

% turbomole run_name

where run_name is any valid UNIX character string used to name your job.

Technical Note: Turbomole creates its own subdirectory (named run_name) in whichto run your job. This subdirectory is created at the beginning of the job, and, if the jobsuccessfully completes, is deleted at the completion of the job (in the case of an unsuc-cessful job, the subdirectory remains). While your job is running the files listed on pageC–1 exist in the subdirectory. At the successful completion of the job, the files aremoved up to your original directory.

Restarting a Turbomole Job

As noted above, if your Turbomole job does not complete successfully, a subdirectory(named run_name) remains. To restart the job from the point at which it was aborted,you can use the -restart option with the turbomole command. For example, if yousubmit a Turbomole job with this command:

% turbomole propyl

8–2 Turbomole

Summary Methodology—Standalone Mode

Met

hodo

logy

and your workstation crashes while the job is running (thus killing your job), the direc-tory from which you launched your job would contain a subdirectory named propyl.You would restart the propyl job with this command:

% turbomole propyl -restart

The -restart option instructs Turbomole to look for (and cd to) the pre-existing subdi-rectory run_name and to pick up where the original job stopped.

If, however, the -restart option is not provided and yet a run_name subdirectory exists,Turbomole appends an underscore (_) and an integer to your run_name, to create asubdirectory with a unique name (in this example, propyl_1). It then starts the job fromthe beginning in the run_name_# subdirectory.

Turbomole A–1

References

A References

Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. “Electronic structure calcula-tions on workstation computers: The program system Turbomole”, Chem. Phys.Lett., 162, 165–169 (1989).

Andrews, J. S.; Jayatilaka, D.; Bone, R. G. A.; Handy, N. C.; Amos, R. D. “Spin con-tamination in single-determinant wavefunctions”, Chem. Phys. Lett., 183, 423–431 (12991).

Andzelm, J.; Baker, J.; Scheiner, A.; Wrinn, M. “A density functional study of chem-ical reactions”, Int. J. Quantum Chem., in press.

Baker, J. “An algorithm for the location of transition states”, J. Comp. Chem., 7, 385(1986).

Baker, J. “Geometry optimization in Cartesian coordinates: Constrained optimiza-tion”, J. Comp. Chem., 13, 240 (1992).

Baker, J. “Techniques for geometry optimization: A comparison of Cartesian and nat-ural internal coordinates”, J. Comp. Chem., in press (1993).

Baker, J.; Bergeron, D. “Constrained optimization in Cartesian coordinates”, J. Comp.Chem., in press (1993).

Baker, J.; Hehre, W. J. “Geometry optimization in Cartesian coordinates: The end ofthe Z-matrix?”, J. Comp. Chem., 12, 606 (1991).

Banerjee, A.; Adams, N.; Simons, J.; Shepard, R. “Search for stationary points on sur-faces”, J. Phys. Chem., 89, 52 (1985).

Becke, A. D. “Density-functional thermochemistry. III. The role of exact exchange”,J. Chem. Phys., 98, 5648–5652 (1993).

Boys, S. F. “Construction of some molecular orbitals to be approximately invariant forchanges from one molecule to another”, Rev. Mod. Phys., 32, 296–299 (1960).

Cerjan, C. J.; Miller, W. H. “On finding transition states”, J. Chem. Phys., 75, 2800(1981).

Chambaud, G.; Levy, B.; Millie, P. Theor. Chim. Acta, 48, 103 (1978).

Cizek; Paldus, J. Chem. Phys., 47, 3976 (1967).

A–2 Turbomole

References

Refe

renc

esCowan, R. D.; Griffin, D. C. “Approximate relativistic corrections to atomic radial

wave functions”, J. Opt. Soc. Am., 66, 1010–1014 (1976).

Császár, P.; Pulay, P. “Geometry optimization by direct inversion in the iterative sub-space”, J. Mol. Struct., 114, 31–34 (1984).

Cundari, T. R.; Stevens, W. J. “Effective core potential methods for the lanthanides”,J. Chem. Phys., 98, 5555–5565 (1993).

Davidson, E. R. J. Chem. Phys., 46, 1833 (1967).

Ditchfield, R. “Self-consistent perturbation theory of diamagnetism. I. A gauge-invari-ant LCAO method for NMR chemical shifts”, Mol. Phys., 27, 789–807 (1974).

Dunning, T. H. “Gaussian basis sets for use in correlated molecular calculations. I. Theatoms boron through neon and hydrogen” J. Chem. Phys., 90, 1007 (1989).

Ehrig, M. Diplomarbeit, Karlsruhe (1990).

Ehrig, M.; Ahlrichs, R. In preparation.

Ermler, W. C.; Ross, R. B.; Christiansen, P. A. “Ab initio relativistic effective poten-tials with spin–orbit operators. VI. Fr through Pu”, Int. J. Quantum Chem., 40,829–846 (1991).

Fletcher, R. Comp. J., 13, 317 (1970).

Fletcher, R. Practical Methods of Optimization, Vol. 1, Unconstrained Optimization,John Wiley & Sons: New York (1980).

Fletcher, R. Practical Methods of Optimization, Vol. 2, Constrained Optimization,John Wiley & Sons: New York (1981).

Fogarasi, G.; Zhou, X.; Taylor, P. W.; Pulay, P. “The calculation of ab initio moleculargeometries: Efficient optimization by natural internal coordinates”, J. Amer.Chem. Soc., 114, 8191 (1992).

Foresman, J.; Head–Gordon, M.; Pople, J.; Frisch, M. J. Phys. Chem., 96, 135 (1992).

Godbout, N.; Salahub, D. R.; Andzelm, J.; Wimmer, E. “Optimization of Gaussian-type basis sets for local spin density functional calculations. I. Boron throughneon, optimization technique and validation”, Can. J. Chem., 70, 560 (1992).

Haase, F.; Ahlrichs, R. “Semidirect MP2 gradient evaluation on workstation comput-ers: The MPGRAD program”, J. Comp. Chem., 14, 907–912 (1993).

Häser, M.; Ahlrichs, R. “Improvements on the direct SCF method”, J. Comp. Chem.,10, 104–111 (1989).

Häser, M.; Ahlrichs, R.; Baron, H. P.; Weis, P.; Horn, H. “Direct computation of sec-ond-order SCF properties of large molecules on workstation computers with anapplication to large carbon clusters”, Theor. Chim. Acta, 83, 455–470 (1992).

Turbomole A–3

References

ReferencesHehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular OrbitalTheory, Wiley Interscience: New York (1986).

Hurley, M. M.; Pacios, L. F.; Christiansen, P. A., Ross, R. B.; Ermler, W. C. “Ab initiorelativistic effective potentials with spin–orbit operators. II. K through Kr”, J.Chem. Phys., 84, 6840–6853 (1986).

Kendall, R. A.; Dunning, T. H.; Harrison, R. J. “Electron affinities of the first-rowatoms revisited. Systematic basis sets and wave functions”, J. Chem. Phys., 96,6796 (1992).

Koga, T.; Kobayashi, H. “Exponent optimization by uniform scaling technique”, J.Chem. Phys., 82, 1437–1439 (1985).

LaJohn, L. A.; Christiansen, P. A.; Ross, R. B.; Atashroo, T.; Ermler, W. C.; “Ab initiorelativistic effective potentials with spin–orbit operators. III. Rb through Xe”, J.Chem. Phys., 87, 2812–2824 (1987).

Mulliken, R. S. “Electronic population analysis on LCAO–MO molecular wave func-tions. I” and “Electronic population analysis on LCAO–MO molecular wavefunctions. II. Overlap populations, bond orders, and covalent bond energies”, J.Chem. Phys., 23, 1833–1846 (1955).

Pacios, L. F.; Christiansen, P. A. “Ab initio relativistic effective potentials with spin-orbit operators. I. Li through Ar”, J. Chem. Phys., 82, 2664 (1985).

Pople, J. A.; Nesbet, R. K. “Self-consistent orbitals for radicals”, J. Chem. Phys., 22,571 (1954).

Pople, J. A. et al., J. Chem. Phys., 96, 135–149 (1992).

Press, W. H.; Flannery, B. P.; Tuekolsky, S. A.; Vetterling, W. T. Numerical Recipes,The Art of Scientific Computing, Cambridge University Press: New York (1986).

Pulay, P., Chem. Phys. Lett., 73, 393 (1980).

Pulay, P., “Improved SCF convergence acceleration”, J. Comp. Chem., 3, 556 (1982).

Pulay, P.; Fogarasi, G.; Pang, F.; Boggs, J. E. “Systematic ab initio gradient calculationof molecular geometries, force constants, and dipole moment derivatives”, J. Am.Chem. Soc., 101, 2550–2566 (1979).

Roby, K. R. “Quantum theory of chemical valence concepts. I. Definition of the chargeon an atom in a molecule and of occupation numbers for electron density sharedbetween atoms”, Mol. Phys., 27, 81–104 (1974).

Roothaan, C. C. J. “Self-consistent field theory for open shells of electronic systems”,Revs. Mod. Phys., 32, 179–194 (1960).

Ross, R. B.; Powers, J. M.; Atashroo, T.; Ermler, W. C.; LaJohn, L. A.; Christiansen,P. A., “Ab initio relativistic effective potentials with spin–orbit operators. IV. Csthrough Rn”, J. Chem. Phys., 93, 6654–6670 (1990).

A–4 Turbomole

References

Refe

renc

esSchäfer, A.; Horn, H.; Ahlrichs, R. “Fully optimized contracted Gaussian basis sets for

atoms Li to Kr”, J. Chem. Phys., 97, 2571–2577 (1992).

Schlegel, H. B. “Optimization of equilibrium geometries and transition structures”, J.Comp. Chem., 3, 214–218 (1982).

Schlegel, H. B. “Estimating the Hessian for gradient-type geometry optimizations”,Theor. Chim. Acta, 66, 333–340 (1984).

Weiss, H.; Ahlrichs, R.; Häser, M., J. Chem. Phys. (in press).

Turbomole B–1

GlossaryB Glossary

Table B–1. Symbols Used in Equations

symbol definition (page)

λ shift parameter (page 2–4), Lagrange multiplier (page 2–6)φ (r) atomic basis function (page 5–13)b eigenvalue (page 2–4)C constraint (page 2–5)e error vector (page 2–8)E energyg gradient vector (page 2–8)H Hessian matrix (page 2–4)m number of constraints (page 2–5)u eigenvector (page 2–4)x geometry (page 2–7)

Table B–2. Definitions of Terms

term page

ECP effective core potentialEF eigenvector-following (page 2–3)RHF restricted Hartree–Fock calculation/wavefunctionSAO symmetry-adapted orbitalUHF unrestricted Hartree–Fock calculation/wavefunction

B–2 Turbomole

Glossary

Glo

ssar

y

Turbomole C–1

Files

C Files

Introduction

This appendix explains the purpose and format of the files used by the Turbomole pro-gram. “Generic” files (i.e., files used by several Biosym/MSI programs) are describedin a separate File Formats book; information specific to the Turbomole program isincluded in this Appendix. Samples of some files are also included.

• .input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page C–7

• .turbo_archive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .page C–7;

• .car. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (generic)

• .arc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (generic)

• .hessian . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (generic)

• _route.csh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page C–11

• .sum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page C–12

• .outmol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . page C–17

• Density of states information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (generic)

The files included here are from a Turbomole calculation on the methyl amine mole-cule. The calculation was done at the Hartree–Fock level of theory with an svp basisset and consisted of a geometry optimization followed by a vibrational frequency com-putation. Additionally, calculation of all available properties was activated. Thus, the.sum file contains results for all four population analyses, static and frequency-depen-dent polarizabilities, NMR shieldings, and excitation energies and oscillator strengths,in addition to the optimized geometry and harmonic vibrational spectrum.

File Contents

Input is provided to Turbomole from the files:

• run_name.input - keyword-style input file.

• run_name.car - standard Biosym .car file (optional, depending on how geometry isprovided, see Geometry keyword in Appendix E).

C–2 Turbomole

The .input File Files

File

s• run_name.mdf - standard Biosym .mdf file (optional).

At the completion of your job, the results of the calculation are written to the file:

run_name.sum

while the complete Turbomole output is written to the file:

run_name.outmol

as your job is running.

Other files which may be written by your job (but whose contents you would normallynot need to view) include:

• run_name.arc - History of Cartesian coordinates from each step of a geometry opti-mization job. Can be used for viewing a trajectory in the Insight interface.

• run_name.car - car file with final molecular coordinates from geometry optimiza-tion jobs.

• run_name.*.grd - 3D volumetric grid data (of MOs, electron density, etc.). Can beused for visualizing MOs, density, etc. in the Insight interface.

• run_name.hessian - Hessian matrix from geometry optimization or vibrational fre-quency jobs (written in Discover Hessian file format - see File Formats book).

• run_name.localized_mo - Localized MOs from Boys orbital localization calcula-tion.

• run_name.orig.car - car file with starting Cartesian coordinates from geometryoptimization jobs.

• run_name_route.csh - An executable list of the steps that will be run, based on theinformation in run_name.input.

• run_name.turbo_archive - Archive of Turbomole job (Turbomole control file for-mat).

The .input File

The Turbomole .input file consists of keywords and their associated options whichdirect the calculation and provide options for various aspects of the calculation.

Only one keyword and its associated options may appear on a line of the .input file.

The keywords in the .input file are case-insensitive (i.e., you may use upper- and/orlowercase characters interchangeably).

Comment lines (specified by beginning the line with “#”) and blank lines are ignored.

Turbomole C–3

Files The .input File

Files.input file keywords and options are fully described in Appendix E, Commands—Stan-dalone Mode and summarized according to function in Chapter 7, Keywords Sum-mary—Standalone Mode.

Sample .input Files

The following .input file shows both the file’s format and the default values for all key-words.

# Defaults File for Turbomole

Product TurbomoleVersion 950

# Primary Job Keywords

Calculate energyMethod hfBasis svGeometry car angsSymmetry C1Spin restrictedCharge 0Multiplicity 1

# DFT Specifications

Functionals vwnIntegration_Grid medium

# Environment

Point_Charges offElectric_Field off

# Molecular Properties

Electrostatic_Moments offBoys_Localization offStatic_Polarizability offFreq_Dep_Polarizability offNMR_Shielding offRelativistic_Correction offPopulation_Analysis offExcitation_Energy offPlot off

C–4 Turbomole


File

sGrid grid1 points 25 range 1.449760 15.038722 grid2 points 25 range -6.350144 6.711650 grid3 points 25 range -1.755567 10.445283

# Additional Job Control

MO_Guess huckelBasis_Type 5d/7fECP off

# Disk and Core Memory Use in MB

AO_Integral_Filesize 0MO_Integral_Filesize 150Max_Core_Memory 20

# SCF Tolerances, Limits & Convergence Criteria

SCF_Energy_Convergence 1e-7SCF_Density_Convergence 1e-5Damping autoSCF_Iterations 30DIIS 5Level_Shift auto

# Optimizer

Locate minimumTS_Mode 0Opt_Coordinate_System autoUse_Symmetry onGDIIS 0Max_Displacement 0.3000Hessian_Update defaultOpt_Print 0Gradient_Convergence 0.00030Displacement_Convergence 0.000300Opt_Energy_Convergence 0.000001Opt_Cycles 50

Turbomole C–5

Files The .input File

FilesThe following input file is for the methyl amide calculation.

#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::# Sample .input 9: Complete input file for CH3NH2#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Title Turbomole input file for the CH3NH2 molecule. Thu Mar23 18:48:01 1995

Product TurbomoleVersion 950

# == Primary Job Keywords ==

Calculate optimize_frequencyMethod hfBasis svpGeometry xyz angC 0.584574699 0.009450559 -0.000000000N -0.852104127 0.343642563 0.000000000H 0.741870761 -1.085527062 -0.000000000H 1.087774396 0.425487757 0.893070102H 1.087774396 0.425487757 -0.893070102H -1.324945092 -0.059270799 -0.818236530H -1.324945092 -0.059270799 0.818236530end_geomSymmetry CsSpin restrictedCharge 0Multiplicity 1

# == Environment ==

Point_Charges offElectric_Field off

# == Molecular Properties ==

Electrostatic_Moments onBoys_Localization onStatic_Polarizability onFreq_Dep_Polarizability onFrequencies 0.875 0.625 0.552 0.284NMR_Shielding onRelativistic_Correction onMulliken_Analysis onLoewdin_Analysis onRoby_Davidson_Analysis on

C–6 Turbomole


File

sESP_Charges onExcitation_Energy onExcited_State_Method rpaExcited_State_Symmetry defaultExcited_State_Multiplicity singletNumber_of_Excited_States 5Plot density potential homo lumo local_homoPlot orbital 8 12 15Plot local_orbital 3 6Grid grid1 points 25 range -6.283235 5.835047 grid2 points 25 range -5.830800 4.583507 grid3 points 25 range -5.467110 5.467110

# == Additional Job Control ==

MO_Guess huckelBasis_Type autoECP off

# == Disk and Core Memory Use in MB ==

AO_Integral_Filesize 10MO_Integral_Filesize 20Max_Core_Memory 32

# == SCF Tolerances, Limits & Convergence Criteria ==

SCF_Energy_Convergence 0.0000001000SCF_Density_Convergence 0.0000100000Damping autoSCF_Iterations 30DIIS 5Level_Shift auto

# == Optimizer Tolerances & Convergence Controls ==

Locate minimumOpt_Coordinate_System autoOpt_Use_Symmetry onGDIIS offMax_Displacement 0.300000Hessian_Update BFGS

Turbomole C–7

Files .turbo_archive (control) File

FilesOpt_Print 2Gradient_Convergence 0.000300Displacement_Convergence 0.000300Opt_Energy_Convergence 0.000001ICONS 0

.turbo_archive (control) File

The .turbo_archive file (also called control file) acts as both a source of input to Tur-bomole and an archive of the results of a Turbomole job. Although in previous versionsof Turbomole, you needed to create and edit the control file to control your Turbomolejob, this is no longer so. All user input is provided via the .input file which from whicha control file is automatically created. Thus, except in very unusual circumstances, youshould not need to edit or look at the .turbo_archive (control) file. At the successfulcompletion of the Turbomole job, the control file is renamed run_name.turbo_archiveand can be used in future Turbomole jobs for providing starting MOs or for readingbasis set/ECP data.

An abbreviated version of the final .turbo_archive file from the methyl amine calcula-tion is included below.

$operating system unix$printlevel 2$coord file=ch3nh2.car type=car$scfintunit unit=30 size=7 file=ch3nh2.twoint$scfdump$lock off$titleturbomole input file for the ch3nh2 molecule. thu mar 23 18:48:01 1995$scfdamp start=0.500 step=0.050 min=0.100$symmetry cs$charge 0$multiplicity 1$pople AO# $scfconv 1.00e-07# $denconv 1.00e-05$scfconv 1.00e-09$denconv 1.00e-07$scfiterlimit 30$aofilesize 10$mofilesize 20$maxcor 32$scfdiis emaxiter 5$scforbitalshift automatic 0.1$mointunit type=intermed unit=61 size=6 file=ch3nh2.halfint type=1111 unit=62 size=3 file=ch3nh2.moint#0 type=1112 unit=63 size=3 file=ch3nh2.moint#1 type=1122 unit=64 size=3 file=ch3nh2.moint#j type=1212 unit=65 size=3 file=ch3nh2.moint#k type=1212a unit=70 size=2 file=ch3nh2.moint#a type=gamma#1 unit=71 size=2 file=ch3nh2.gamma#1 type=gamma#2 unit=72 size=2 file=ch3nh2.gamma#2$hessian file=ch3nh2.hessian type=discover$hessian (projected) file=ch3nh2.hessian_projected$amatrix$properties

C–8 Turbomole

.turbo_archive (control) File Files

File

s population analysis active fit active cowan-griffin active moments/trace active localization active plot active$mulliken$loewdin$paboon momao$vdw_fit shell 4000 1.0 shell 4000 2.0 shell 4000 3.0 shell 4000 4.0 shell 4000 6.0 shell 4000 8.0 shell 4000 10.0 shell 4000 12.0 shell 4000 14.0 shell 4000 16.0 shell 4000 20.0 shell 4000 24.0 shell 4000 32.0$hyperpolscfconv 1.0d-04$boys lmofile=ch3nh2.localized_mo all locxyz x y z sweeps 10000# $scfinstab dynpol 0.032156 0.022969 0.020286 0.010437$scfinstab rpas 5$grid insight mo density outfile=ch3nh2_DENS.grd origin 0.0 0.0 0.0 vector1 1.0 0.0 0.0 vector2 0.0 1.0 0.0 vector3 0.0 0.0 1.0 grid1 points 25 range -6.283235 5.835047 grid2 points 25 range -5.830800 4.583507 grid3 points 25 range -5.467110 5.467110## additional $grid entries deleted#$scfmo scfconv=9 format(4d20.14)# molecular orbitals of project :# ---> turbomole input file for the ch3nh2 molecule. thu mar 23 18:48:0 <---# SCF total energy is -95.1455879966 a.u.# 1 a’ eigenvalue=-.15529958729802D+02 nsaos=34 .19789374843672D-03-.59019785500835D-03 .10355589908286D-01 .35098324790644D-03-.18406799013752D-03-.33233392620382D-02 .11438976389672D-02 .50775414238425D-03 .51863648912135D-03-.79925376687210D-03-.99036064886231D+00 .36428768021626D-01-.20659112932425D-01 .29849159759132D-03 .26931055301418D-02-.42111984224639D-02 .17408069608540D-02 .82908431347262D-03 .62723517034340D-03 .23579306825102D-03-.51686866255849D-03-.10076140569629D-02 .14310445083358D-03-.48589034184775D-04-.95189958999763D-03-.14979664890727D-02 .35568060506708D-05-.87552913896124D-06 .84484189017153D-04-.27568237392916D-02 .30938709997452D-02-.11771374860256D-02-.15049374673154D-02-.28927460093502D-02## additional $scfmo data deleted#$atomsc 1 \ basis =c svpn 2 \

Turbomole C–9

Files .turbo_archive (control) File

Files basis =n svph 3-7 \ basis =h svp$basis*c svp* 5 s 1238.4016938 .54568832082E-02 186.29004992 .40638409211E-01 42.251176346 .18025593888 11.676557932 .46315121755 3.5930506482 .44087173314 1 s .40245147363 1.0000000000 1 s .13090182668 1.0000000000 3 p 9.4680970621 .38387871728E-01 2.0103545142 .21117025112 .54771004707 .51328172114 1 p .15268613795 1.0000000000 1 d .80 1.00*h svp* 3 s 13.010701 .19682158E-01 1.9622572 .13796524 .44453796 .47831935 1 s .12194962 1.0000000 1 p .80 1.00*n svp* 5 s 1712.8415853 -.53934125305E-02 257.64812677 -.40221581118E-01 58.458245853 -.17931144990 16.198367905 -.46376317823 5.0052600809 -.44171422662 1 s .58731856571 1.0000000000 1 s .18764592253 1.0000000000 3 p 13.571470233 -.40072398852E-01 2.9257372874 -.21807045028 .79927750754 -.51294466049 1 p .21954348034 1.0000000000 1 d 1.00 1.00*$rundimensions natoms=7 ntrans=2 dim(fock,dens)=1597 nshell=27 nbf(CAO)=55 nbf(AO)=53 dim(trafo[SAO<-->AO/CAO])=79 rhfshells=1$drvopt

C–10 Turbomole

.turbo_archive (control) File Files

File

s cartesian on basis off global off hessian on dipole on nuclear polarizability$statistics off$frequency analytical cs$translation vector -.00000001592770 -.00000000647906 .00000000000000$rotation matrix 1.00000000000000 .00000000000000 .00000000000000 .00000000000000 1.00000000000000 .00000000000000 .00000000000000 .00000000000000 1.00000000000000$closed shells a’ 1-7 ( 2 ) a” 1-2 ( 2 )$last step chemshift$thize .10000000E-04$thime 1$energy SCF SCFKIN SCFPOT -1/3 Tr(alpha) 1 -95.14316666214 94.51717640919 -189.66034307132 2 -95.14548281914 94.66895204505 -189.81443486419 3 -95.14557032919 94.69512247764 -189.84069280683 4 -95.14558337437 94.69781953526 -189.84340290964 5 -95.14558728480 94.69684482474 -189.84243210954 6 -95.14558799439 94.69566864100 -189.84125663539 7 -95.14558799661 94.69560367210 -189.84119166872 -18.38440880548$last SCF energy change = -.22237572E-08$grad cartesian gradients## additional $grad data deleted# cycle = 7 SCF energy = -95.1455879966 |dE/dxyz| = .000201 1.06936940947925 -.01950824960268 .00000000000000 c -1.58417300449566 .63342298323623 .00000000000000 n 1.47080876908860 -2.05554024834791 .00000000000000 h 1.98644523477022 .79516603896239 1.65744090918540 h 1.98644523477022 .79516603896239 -1.65744090918540 h -2.46444782558577 -.07435328443980 -1.52469868682879 h -2.46444782558577 -.07435328443980 1.52469868682879 h -.14309237915103E-03 .75458242885952E-04 .00000000000000E+00 .78653562994708E-04 .29355920178086E-04 .00000000000000E+00 .19850870328655E-04 -.13957291904596E-05 .00000000000000E+00 .21693219408814E-04 -.27060684735958E-04 -.27413535521492E-04 .21693219408814E-04 -.27060684735958E-04 .27413535521492E-04 .60075339725074E-06 -.24648532382043E-04 -.28081208291675E-04 .60075339725074E-06 -.24648532382043E-04 .28081208291675E-04$traloop 1$dipole x -.00090567432473 y -.55359655453327 z .00000000000000$dipgrad cartesian dipole gradients .63658191114524D+00 -.14040144624365D+00 .00000000000000D+00 -.39796542731666D-01 .43787613610178D+00 .00000000000000D+00 .00000000000000D+00 .00000000000000D+00 .22932331476293D+00## additional $dipgrad data deleted#$nuclear polarizability 1/3 Tr(alpha) = 5.9950 Anisotropy = 8.8008 2.16088616 -2.26850704 4.80609028 .00000000 .00000000 11.01798838$vibrational normal modes 1 1 .1249261996 .0524804992 .0323377766 .1440774319 .1303119841 1 2 .1636993441 .0652070133 .0407058159 -.4219332043 .1394224868 1 3 -.3460729035 .2202159769 .1582206009 .3972361010 .2202159769 1 4 .1319638300 .4980206593 .0000000000 .1146712318 -.1857577227 1 5 .0000000000

Turbomole C–11

Files _route.csh File

Files$vibrational spectrum# mode symmetry wave number intensity selection rules# cm**(-1) a.u. IR RAMAN 1 .00 .0000000 - - 2 .00 .0000000 - - 3 .00 .0000000 - - 4 .00 .0000000 - - 5 .00 .0000000 - - 6 .00 .0000000 - - 7 a” 342.00 .0434661 YES YES 8 a’ 902.89 .1744892 YES YES 9 a” 1042.73 .0000493 YES YES 10 a’ 1163.72 .0285784 YES YES 11 a’ 1268.86 .0146205 YES YES 12 a” 1451.23 .0000011 YES YES 13 a’ 1575.18 .0040757 YES YES 14 a’ 1605.60 .0090562 YES YES 15 a” 1621.43 .0022761 YES YES 16 a’ 1784.85 .0250272 YES YES 17 a’ 3127.78 .0958502 YES YES 18 a’ 3222.21 .0590994 YES YES 19 a” 3263.72 .0448085 YES YES 20 a’ 3743.81 .0013761 YES YES 21 a” 3822.82 .0029451 YES YES$polscfmo file = mosxi$polarizability 1/3 Tr(alpha) = 18.3844 Anisotropy = 3.3194 20.08778656 .09151452 16.31278782 .00000000 .00000000 18.75265204$last polarizability change = -18.384409$nmr shielding constants# NO. TYPE MULT. ISOTROPIC ANISOTROPIC CPHF-CONTRIBUTION 1 c 1 240.28456294 20.75849392 1.14973030 2 n 1 303.05088914 32.01162587 -6.35579313 3 h 1 30.33364028 16.42859208 .28547156 4 h 2 30.11749220 14.12313492 .56885902 6 h 2 30.27598058 27.57890855 -1.50213208$end

_route.csh File

The run_name_route.csh file is a shell script that is created and launched by the mainturbomole shell script (after all preliminary job steps have been completed). This fileprovides the route of the actual Turbomole executables that will run during the courseof your job. Except for advanced Turbomole users who may want to modify the jobroute for special cases, you should have no need to modify or look at this file.

#!/bin/csh -fset process = $$execute_job $process TurboGEOMexecute_job $process TurboGUESSexecute_job $process set_stat_flag dscfexecute_job $process TurboSCF@ i = 1set converge = 0@ opt_cycles = 30while (($i <= 30) && !($converge))execute_job $process TurboSCFexecute_job $process TurboGRADexecute_job $process optimize ch3nh2 -hess NONE -energy@ ex_status = $statusif ($ex_status == 0) set converge = 1

C–12 Turbomole

Sample .sum File Files

File

sif ($ex_status > 1) goto get_out@ i++endif ($i > 30) then echo echo “Maximum iterations reached: aborting” echo echo “Maximum iterations completed: optimization aborted” >> ch3nh2.outmol @ ex_status = 2 goto get_outendifexecute_job $process awk -f `qwhich reset_convergence.awk` keyword=’$scfconv’ control > .tmp.ctrlexecute_job $process cp .tmp.ctrl controlexecute_job $process awk -f `qwhich reset_convergence.awk` keyword=’$denconv’ control > .tmp.ctrlexecute_job $process cp .tmp.ctrl controlexecute_job $process TurboSCFexecute_job $process set_stat_flag mpgradexecute_job $process TurboMPGRADexecute_job $process TurboMPGRADexecute_job $process TurboFREQexecute_job $process TurboPOLLYexecute_job $process TurboPROPexecute_job $process TurboXCITEexecute_job $process rm -f ‘nfile*’execute_job $process awk -f `qwhich cvt_ctrl_file.awk` flag=2 control > .tmp.ctrlexecute_job $process cp .tmp.ctrl controlexecute_job $process TurboXCITEexecute_job $process TurboNMRget_out:exit

Sample .sum File

Product: turbomole Job Name: ch3nh2 Calculation Type: Optimize Frequency

Created: Mon Aug 21 13:49:18 1995

Method: hf Basis: svp Symmetry: cs Spin: RESTRICTED Charge: 0 Multiplicity: 1

###############################################################################

============================ Optimized Molecular Geometry ============================

Cartesian Coordinates (Angstrom) Cartesian Gradients (au) -------------------------------- ----------------------------- Atom Mass x y z dE/dx dE/dy dE/dz----- -------- 1 C 12.01115 0.565886 -0.010323 0.000000 -0.000143 0.000075 0.000000 2 N 14.00670 -0.838308 0.335193 0.000000 0.000079 0.000029 0.000000 3 H 1.00797 0.778318 -1.087745 0.000000 0.000020 -0.000001 0.000000 4 H 1.00797 1.051181 0.420784 0.877080 0.000022 -0.000027 -0.000027

Turbomole C–13

Files Sample .sum File

Files 5 H 1.00797 1.051181 0.420784 -0.877080 0.000022 -0.000027 0.000027 6 H 1.00797 -1.304129 -0.039346 -0.806835 0.000001 -0.000025 -0.000028 7 H 1.00797 -1.304129 -0.039346 0.806835 0.000001 -0.000025 0.000028----- -------- ------------------------------- ----------------------------- 31.05770 Total Molecular Mass

================== Molecular Energies ==================

Electronic Energies: -------------------- Total SCF Energy = -95.1455880 Hartree -59704.697 kcal/mol

Cowan-Griffin Relativistic = -0.0418645 Hartree Energy Correction

Nuclear Repulsion Energy = 42.3090553 Hartree

Thermodynamic Energies: ----------------------- Zero Point Vibrational Energy = 42.800 kcal/mol

Standard quantities at 298.18 K and 1.00 ATM

Translational Enthalpy = 0.889 kcal/mol Rotational Enthalpy = 0.889 kcal/mol Vibrational Enthalpy = 43.116 kcal/mol -------------------------------------------------------- Total Enthalpy = 44.894 kcal/mol

Translational Entropy = 36.233 cal/mol.K Rotational Entropy = 19.323 cal/mol.K Vibrational Entropy = 1.540 cal/mol.K -------------------------------------------------------- Total Entropy = 57.096 cal/mol.K

================== Molecular Orbitals ==================

Index Symmetry eV Occ. ---------------------------------- 1 1a’ -422.5950 2.00 2 2a’ -305.9791 2.00 3 3a’ -31.4837 2.00 4 4a’ -24.0518 2.00 5 1a” -18.0272 2.00 6 5a’ -16.4202 2.00 7 6a’ -15.2334 2.00 8 2a” -13.9965 2.00

C–14 Turbomole


File

s 9 7a’ -10.4327 2.00 10 8a’ 4.9005 0.00 11 9a’ 6.1138 0.00 12 3a” 6.7386 0.00 13 10a’ 7.4012 0.00 14 4a” 7.9747 0.00 15 11a’ 10.9125 0.00 16 5a” 17.0737 0.00 17 12a’ 18.0024 0.00 18 13a’ 18.8222 0.00 19 6a” 21.9047 0.00 20 14a’ 23.8342 0.00 -------( Please see .outmol file for entire spectrum )--------

==================== Vibrational Spectrum ====================

harmonic infrared selection frequency intensity rules mode symmetry cm**(-1) km/mol relative IR RAMAN ---- -------- --------- ------------------ ------------ 1 a” 342.00 42.58 24.91 YES YES 2 a’ 902.89 170.93 100.00 YES YES 3 a” 1042.73 0.05 0.03 YES YES 4 a’ 1163.72 28.00 16.38 YES YES 5 a’ 1268.86 14.32 8.38 YES YES 6 a” 1451.23 0.00 0.00 YES YES 7 a’ 1575.18 3.99 2.34 YES YES 8 a’ 1605.60 8.87 5.19 YES YES 9 a” 1621.43 2.23 1.30 YES YES 10 a’ 1784.85 24.52 14.34 YES YES 11 a’ 3127.78 93.89 54.93 YES YES 12 a’ 3222.21 57.89 33.87 YES YES 13 a” 3263.72 43.89 25.68 YES YES 14 a’ 3743.81 1.35 0.79 YES YES 15 a” 3822.82 2.89 1.69 YES YES ---- -------- --------- ------------------ ------------

======================== Atom Centered Properties ========================

Atom Partial Charges (au) Nuclear Shieldings (ppm) ------ ---------------------------------- ------------------------ MUL LOW ESP RD ISO ANISO 1 C 0.1082 -0.2359 0.4251 -0.0139 173.5384 37.9159 2 N -0.3802 -0.3281 -0.9759 -0.1667 266.9638 54.2547 3 H 0.0029 0.0832 -0.0910 0.0051 30.0476 10.3486 4 H 0.0259 0.0974 -0.0323 0.0259 29.9576 9.4666 5 H 0.0259 0.0974 -0.0323 0.0259 29.9576 9.4666 6 H 0.1086 0.1430 0.3532 0.0619 32.5821 16.5912 7 H 0.1086 0.1430 0.3532 0.0619 32.5821 16.5912

Turbomole C–15

Files Sample .sum File

Files ------ ---------------------------------- ------------------------

==================== Molecular Properties ====================

Electrostatic Moments ---------------------

Dipole Moment (Debye) --------------------- <x>: -0.002302 <y>: -1.407113 <z>: 0.000000

1.4071 Debye

Non-Zero Cartesian Moments (Debye/Angstrom units) ------------------------------------------------- <xx>: -13.088153 <yy>: -15.995144 <zz>: -12.523811 <xy>: 1.886230 <xxx>: 0.784652 <yyy>: -6.771212 <xxy>: -3.230482 <yyx>: 2.834838 <zzx>: -0.607258 <zzy>: -1.405456 <xxxx>: -68.168137 <yyyy>: -26.970462 <zzzz>: -22.559165 <xxxy>: 7.194430 <yyyx>: 6.479365 <xxyy>: -18.014739 <xxzz>: -12.927833 <yyzz>: -8.379272 <zzxy>: 2.556539

Polarizabilities (au) ---------------------

Static Polarizability Tensor ---------------------------- x y z x 20.08779 y 0.00000 16.31279 z 0.00000 0.00000 18.75265 ----------------------------------------------- Isotropic Static Polarizability = 18.38441 Anisotropy of Static Polarizability = 3.31937

First Static Hyperpolarizability Tensor --------------------------------------- xxx: -23.68650 yyy: 45.98392 zzz: 0.00000 xxy: 13.60000 xxz: 0.00000 xyy: -24.38814 yyz: 0.00000 xzz: -2.74697 yzz: -10.24595 xyz: 0.00000

Frequency Dependent Polarizability Tensor - Frequency = 0.8750 eV ------------------------------------------------------------------ x y z

C–16 Turbomole


File

s x 20.18188 y 0.00450 16.63930 z 0.00000 0.00000 18.81220 --------------------------------------------- Isotropic F.D. Polarizability = 18.54446 Anisotropy of F.D. Polarizability = 3.09415

Frequency Dependent Polarizability Tensor - Frequency = 0.6250 eV ------------------------------------------------------------------ x y z x 20.15520 y 0.00493 16.61455 z 0.00000 0.00000 18.78635 --------------------------------------------- Isotropic F.D. Polarizability = 18.51870 Anisotropy of F.D. Polarizability = 3.09248



============== Excited States ==============

Method: RPA Symmetry: a’ Spin: singlet ----------------------------------------------- Oscillator State Energy (eV) Strength (au) ----- ----------- -------------

Turbomole C–17

Files .outmol File

Files 1 7.8796 0.0080 2 10.1068 0.0872 3 11.3081 0.1467 4 12.0484 0.1094 5 12.1573 0.0203 ----- ----------- -------------

============== Job Statistics ==============

Mon Aug 21 13:49:19 PDT 1995 Computer: ibm10 CPU: ibm Optimization Cycles: 6 Time: 2247.0u 166.0s 49:59

.outmol File

The .outmol file contains the complete output from each of the Turbomole executablesrun during the course of your Turbomole job. You usually do not need to refer to the.outmol file, since the results of the job are tabulated and presented in the .sum file.Since the .sum file is not created until the job completes, you may, however, want toview the .outmol file during job execution to monitor progress. In addition, if you needto access some detail of the calculation that is not reported in the .sum file, you canrefer to the .outmol file.

C–18 Turbomole

.outmol File Files

File

s

Turbomole D–1

Utilities

D Utilities

See also Chapter 3, Implementation, for the components of the Turbomole product.

Background Jobs

Much of the computational work of Biosym/MSI products is performed by back-ground jobs that are run using the Insight user interface. Background jobs run concur-rently with the Insight program; this is possible because, once started, they do notrequire user interaction. If you have access to more than one computer (mainframe orworkstation), you may want to run some background jobs on a different computer (theremote host) than the one that is running Insight (the local host).

Several general requirements for running a background job on a remote host are:

• The actual background job program must exist as an executable image for that host.

• Files transferred between local and remote hosts must be readable and writable onboth hosts.

• You must have an account on the remote host, as well as sufficient disk space tocontain all the input, temporary, and output files produced by that background job.

• The local host must be able to communicate statuses, submit jobs, and copy files tothe remote host.

Making an executable image compatible with a remote host involves recompiling andrelinking the program; this is done by Biosym/MSI for host types that the companysupports.

The Network Queuing System and Background Jobs

Background jobs are often started from the Insight interface in immediate submissionmode; that is, the job is run on the selected machine immediately upon submission.However, background jobs can also be submitted to a queue. The queueing mechanismpulls jobs from the queue and starts them on one of the machines available for thequeue. Typically, each job is run to completion before the next job is pulled off thequeue. Support for the network queuing system (NQS) is now available to allow youto submit background jobs to a queue on a local or remote machine.

D–2 Turbomole

Background Jobs Utilities

Utili

ties

It is up to you to acquire and install NQS products and deal with its support issues. TheBackground_Job queueing mechanism assumes a properly configured NQS.

Turbomole E–1

Comm

ands

E Commands—Standalone Mode

The following sections contain a complete description of the commands used in theconstituent programs of Turbomole: These commands (keywords) are supplied to theTurbomole program from the input file, as described in Chapter 8, Methodology—Standalone Mode and Appendix C, Files.

The commands are listed according to function in Table E–1 below and in Chapter 7,Keywords Summary—Standalone Mode.They are described fully in alphabetical orderstarting on page E–8.

Turbomole .input file

The Turbomole .input file consists of keywords and their associated options whichdirect the calculation and provide options for various aspects of the calculation. Key-words that do not explicitly appear in the .input file are set to their default values. Onlyone keyword and its associated options may appear on a line of the .input file.

The keywords in the .input file are case-insensitive (i.e., you may use upper- and/orlowercase characters interchangeably). Comment lines (specified by beginning the linewith “#”) and blank lines are ignored.

A typical .input file would look like:

# Commentkeyword_1 option_1keyword_2 option_2# Commentkeyword_3 option_3 . . .

Examples of complete .input files are located in Appendix C, Files.

.input file keywords and options are listed in the following table. More detailed infor-mation on keyword and option usage follows on page E–8.

E–2 Turbomole

Commands—Standalone Mode

Com

man

ds

Table E–1. Summary of Keywords/Options

Keyword Option(s) Meaning

Header Keywords (used for job identification purposes only)Title string Provide job title.Product DMol Identify which Biosym quantum product is being

run.TurbomoleZindo

Version 950 Identify version of product.Primary Job Control KeywordsCalculate energy (default) Select calculation to be run.

gradientoptimizefrequencyoptimize_frequencynumfreqoptimize_numfreq

Method ACM Select quantum method.DFTHF (default)MP2

Basis string (default= sv)

Select basis set.

file stringby_elementby_number

Geometry car (default) ang(default)

Specify molecular geometry and units.

bohrxyz ang

(default)bohr

zmatSymmetry auto (default) Specify molecular symmetry.

stringSpin restricted

(default)Select method for treating spin portion of wavefunc-

tion.restricted_openunrestricted

Charge integer Specify total molecular charge.

Turbomole E–3


Comm

ands

Multiplicity positiveinteger

Specify total spin multiplicity.

Additional Job Control KeywordsMO_Guess huckel (default) Specify initial SCF MOs.

corestring

Swap_Orbitals pair(s) ofintegers

Modify default orbital occupations.

Swap_Alpha_Orbitals

pair(s) ofintegers

Modify default alpha orbital occupations for unre-stricted spin states.

Swap_Beta_Orbitals

pair(s) ofintegers

Modify default beta orbital occupations for unre-stricted spin states.

Basis_Type auto (default) Select representation of d- and f- type basis func-tions.5d/7f

6d/10fECP off (default) Activate use of effective core potentials.

onECP_Range Li-Pu Select which elements will be assigned effective

core potentials.Na-PuK-PuRb-Pu (default)


integer (default= 0)

Specify the amount of disk space (in MBytes) to beused for storing AO 2-electron integrals.



Specify the amount of disk space (in MBytes) to beused for storing MO 2-electron integrals.

Max_Core_Memory


Specify the amount of in-core memory (in MBytes)to be used for holding A-matrix elements duringCPHF.

Step_Size real (default= 0.005)

Specify the finite difference step-size to take infinite-difference numerical frequency calculations.

DFT Specific KeywordsFunctionals ACM Select density functionals.

B88BLYPBPBVWNSLATERSVWN (default)



E–4 Turbomole


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ds

ACM_Coeffs slater real (default= 0.8)

Specify ACM coefficients.

vwn real (default= 1.0)

b88 real (default= 0.72)

pw real (default= 0.81)

Integration_Grid xfine Specify integration grid.finemedium (default)coarsexcoarse

Keywords for Controlling External EnvironmentPoint_Charges off (default) Provide external point charges in file string.

stringElectric_Field off (default) Provide x,y,z components of external electrostatic

field.real1 real2 real3Keywords Controlling Calculation of PropertiesElectrostatic_

Momentsoff (default) Activate calculation of dipole, 2nd, 3rd, and 4th Car-

tesian electrostatic moments.on

Boys_Localization

off (default) Activate Boys MO localization.

onStatic_

Polarizabilityoff (default) Activate calculation of electrostatic polarizability +

1st hyperpolarizability.on


off (default) Activate calculation of frequency-dependent polar-izability tensor(s).

onFrequencies real(s) (default =

0.6491 1.17)Provide frequency(ies) at which to calculate fre-

quency-dependent polarizability tensor(s).NMR_Shielding off (default) Activate calculation of nuclear magnetic shielding

tensors.onRelativistic_

Correctionoff (default) Activate calculation of Cowan-Griffin relativistic cor-

rection to SCF energy.on

Mulliken_Analysis

off (default) Activate calculation of Mulliken population analysis.

on



Turbomole E–5


Comm

ands

Loewdin_Analysis

off (default) Activate calculation of Loewdin population analysis.

onRoby_Davidson_

Analysisoff (default) Activate calculation of Roby–Davidson population

analysis.on

ESP_Charges off (default) Activate calculation of atomic charges.on

Excitation_Energy off (default) Activate calculation of excited-state transition ener-gies and oscillator strengths.on


sci (default) Select method of excited-state calculation.

rpaExcited_State_

Symmetrydefault (default) Specify spatial symmetry of excited state(s).

stringExcited_State_

Multiplicitysinglet (default) Specify spin multiplicity of excited state(s).

tripletNumber_Of_

Excited_Statesinteger (default

= 1)Specify the number of excited states to calculate.

Plot off (default) Activate generation of 3D grid data for subsequentvisualizing in Insight interface.or one of more of:

densitypotentialhomolumolocal_homoorbital integer(s)local_orbital

integer(s)Grid grid_

specificationsDefine 3D rectangular region for plotting (see Plot

keyword, page E–64).Keywords for SCF Tolerances and Convergence ControlSCF_Energy_

Convergencereal (default =

10^-7)Specify SCF energy convergence criterion.


real (default =10^-5)

Specify SCF density convergence criterion.

Damping auto (default) Specify SCF damping procedure.offreal



E–6 Turbomole


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SCF_Iterations integer (default= 30)

Specify maximum number of SCF iterations to carryout.

DIIS integer (default= 5)

Specify maximum number of SCF iterations to savefor DIIS procedure.

offLevel_Shift real (default =

0.1)Specify virtual orbital level shift procedure.

offKeywords for Control of Geometry OptimizationLocate minimum (default) Select type of stationary point to which to optimize.

transition_stateOpt_Coordinate_

Systemauto (default) Select type of coordinate system in which to opti-

mize.internalcartesian

Opt_Use_Symmetry

on (default) Activate symmetry use during geometry optimiza-tion.

offGDIIS off (default) Activate GDIIS during optimization.

autointeger

Max_Displacement

real (default =0.3)

Specify maximum step size for optimizer.

Hessian_Update Powell (defaultfor transitionstates)

Select Hessian matrix update method for optimizer.

BFGS (defaultfor minima withGDIIS off)

BFGS_safe(default forminima withGDIIS on)

noneHessian_File none (default) Specify initial Hessian matrix for optimizer.

stringGradient_


0.0003)Specify maximum gradient convergence criterion

for optimizer.Displacement_


0.0003)Specify maximum displacement convergence crite-

rion for optimizer.Opt_Energy_


0.000001)Specify energy convergence criterion for optimizer.



Turbomole E–7


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Format for Documenting Turbomole Keywords

The rest of this chapter contains detailed descriptions of each of the keywords avail-able in the standalone version. For each command, documentation is divided into sub-sections:

• Options, including syntax and keyword summary.

• Description and example

Conventions used in documenting the commands are described below, along with ashort description of the intent of each subsection.

Syntax

The Options subsection begins with the command options and syntax presented in asgeneric a form as possible. Several type style conventions are used to distinguish dif-ferent kinds of words.

Words (or letters) in bold and not italicized indicate the names of keywords that mustbe typed exactly as shown. However, they are case-insensitive and may be typed inlower-, upper-, or mixed case.

Words in bold italics indicate options that must be replaced with appropriate text, asindicated in the lists of allowed values for each keyword.

The values appropriate to each keyword are also listed, and may be (as appropriate)numbers or enumerated constants:

• Numbers can be represented in integral, floating-point, or exponential form. Tur-bomole converts the number to the appropriate form, depending on the context.

Opt_Cycles integer(default = 50)

Specify maximum number of optimization cycles tocarry out.

Constraint_Method lagrange Select method for handling geometric constraintsduring optimization.penalty

lagrange/penalty(default)

penalty/lagrangeCONSTRAINT constraint

specificationsDefine distances, angles, dihedral angles to be con-

strained during geometry optimization.FIXED fix coordinate

specificationsDefine Cartesian coordinates to fix during geometry

optimization.



E–8 Turbomole

ACM_Coeffs Commands—Standalone Mode

Com

man

ds• Mutually exclusive options are represented by enumerated constants identified by

names. For example, the Calculate command keyword can be set to values ofenergy, gradient, optimize, frequency, optimize_frequency, numfreq, oroptimize_numfreq, and nothing else. The names of enumerated constants must notbe enclosed in quotation marks.

Detailed Descriptions of Keywords/Options

ACM_Coeffs

Options (specify all):

slater real (default=0.8)

vwn real (default = 1.0)

b88 real (default = 0.72)

pw real (default = 0.81)

Description and Example

The ACM_Coeffs keyword is used to provide the linear mixing coefficients for eachof the components of the exchange-correlation energy (Exc) expression of the adiabaticconnection method, for example:

ACM_Coeffs slater 0.71 vwn 1.0 b88 0.72 pw 0.81

The ACM Exc expression is:

Where:

ExSlater = Slater local exchange energy

Exexact = exact Hartree-Fock exchange energy

EcVWN = VWN local correlation energy

ExB88 = Becke-88 non-local exchange energy

EcPW = PW-91 non-local correlation energy

Exc

aSESlaterx

1 aS–( ) Eexactx

aVEVWNc

aBEB88x

aPEPWc

+ + + +=

Turbomole E–9

Commands—Standalone Mode AO_Integral_Filesize

Comm

andsAnd the options provide the coefficients as follows:

slater real

real provides the value for aS

vwn real

real provides the value for aV

b88 real

real provides the value for aB

pw real

real provides the value for aP

Note that the default values for these coefficients yield the original ACM scheme pro-posed by Becke (1993). Also note that, while it is possible to give any value to each ofthe coefficients, values less than 0.0 or greater than 1.0 make no sense within the con-text of the adiabatic connection method and should, therefore, be avoided.

Thus, to specify that Turbomole use the following ACM functional:

You would include the following line in your input file:

ACM_Coeffs slater 0.71 vwn 1.0 b88 0.72 pw 0.81


Options:

integer (default = 0)


The AO_Integral_Filesize keyword is used to specify the amount of disk space (inMBytes) to use for storing AO two-electron integrals, e.g., to use 60 MBytes of diskspace to store AO two-electron integrals you would input:

AO_Integral_Filesize 60

The default value of 0 would utilize no disk space for two-electron AO integral storage(i.e., a fully direct SCF), and these integrals would be re-calculated as needed. It is usu-

Exc

0.71ESlaterx

0.29Eexactx

EVWNc

0.72EB88x

0.81EPWc

+ + + +=

E–10 Turbomole

Basis Commands—Standalone Mode

Com

man

dsally most efficient (in terms of CPU time) to run in a semi-direct way (i.e., specify anon-zero value for integer), so that the larger, more expensive integrals are calculatedonce and stored and the remaining integrals are recalculated as needed.

Basis

Options (select one):

string (default = sv)

by_element

by_number

file string

The syntaxes for the by_element and by_number options are:

by_element atomic symbol = string atomic symbol = string ... = ...endbasis

by_number integer(s) = string integer(s) = string ... = ...endbasis


The Basis keyword is used to select the atomic basis sets to use in your calculation.You provide one of the options from to list above, for example:

Basis tz2p

where the usage of the options is described below.

The Basis string usage instructs Turbomole to fetch the basis set named in string fromthe basis set library and assign that basis set to all atoms in your molecule. Basis setsavailable in the library include the following (Please refer to the Turbomole basis setlibrary files in $BIOSYM/data/turbomole/bases/ for explicit basis set specifications.):

Turbomole E–11

Commands—Standalone Mode Basis

Comm

andssv

Split-valence (valence double-zeta), Hartree-Fock atom-optimized basis setfrom Schaefer et al. (1992). Available for H-Kr.

svp

Split-valence basis set plus one set of polarization functions per atom. Refer topage 5–9 ff. for polarization orbital exponents. Available for H-Kr.

dz

Double-zeta, Hartree-Fock atom-optimized basis set from Schaefer et al.(1992). Available for H-Kr.

dzp

Double-zeta basis set plus one set of polarization functions per atom. Availablefor H-Kr.

tz

Triple-zeta, Hartree-Fock atom-optimized basis set from Schaefer et al. (1992).Available for H-Ar.

tzp

Triple-zeta basis set plus one set of polarization functions per atom. Availablefor H-Ar.

tz2p

Triple-zeta basis set plus two sets of polarization functions per atom. Availablefor H-Ar.

sto-3g

The standard STO-3G, Hartree-Fock atom-optimized basis sets for H-Xe(Hehre et al. 1986 and references therein).

3-21g

The standard 3-21G, Hartree-Fock atom-optimized basis sets for H-Ar (Hehreet al. 1986 and references therein).

6-31g

The standard 6-31G, Hartree-Fock atom-optimized basis sets for H-Ar (Hehreet al. 1986 and references therein).

6-31g*

The 6-31G basis sets plus one set of polarization functions on Li-Ar; the 6-31Gbasis set on H and He. Refer to page 5–9 ff. for polarization orbital exponents.

E–12 Turbomole


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ds6-31g**

The 6-31G basis sets plus one set of polarization functions on H-Ar. Refer topage 5–9 ff. for polarization orbital exponents.

dzvd

Valence double-zeta local DFT atom optimized basis set for H-Xe + one set ofpolarization functions per atom for all atoms except H, He (Godbout et al.1992).

dzvp

Valence double-zeta local DFT atom optimized basis set for H-Xe + one set ofpolarization functions per atom (Godbout et al. 1992).

tzvp

Valence triple-zeta local DFT atom optimized basis set for H, B-F, Al-Ar + oneset of polarization functions per atom (Godbout et al. 1992).

cc-pvdz

Correlation-consistent polarized valence double-zeta basis set for H, He, B-F(Dunning 1989).

aug-cc-pvdz

Correlation-consistent polarized valence double-zeta basis set for H, He, B-Faugmented with diffuse functions (Kendall et al. 1992).

cc-pvtz

Correlation-consistent polarized valence triple-zeta basis set for H, He, B-F(Dunning 1989).

aug-cc-pvtz

Correlation-consistent polarized valence triple-zeta basis set for H, He, B-Faugmented with diffuse functions (Kendall et al. 1992).

unc-aug-cc-pvtz

Uncontracted correlation-consistent polarized valence triple-zeta basis set forH, He, B-F, Al-Ar augmented with diffuse functions (Kendall et al. 1992, Woonand Dunning 1993).

For flexibility in assigning basis sets, the by_element and by_number options can beused, or you can read in basis sets from your own file.

The by_element option is used to assign a unique basis set to each element type (iden-tified by atomic symbol). For example, for a molecule consisting of C, N, O, H, and Cratoms, the following Basis input:

Turbomole E–13


Comm

andsBasis by_element C,N = dzp O = tz2p H = sv Cr = dzend_basis

assigns the dzp basis set to all C, N atoms in the molecule, the tz2p basis set to all Oatoms in the molecule, the sv basis set to all H atoms in the molecule, and the dz basisset to all Cr atoms in the molecule.

Technical Notes:

• The equal signs (=) are required separators between the atomic symbol(s) and thebasis set name.

• The end_basis line is required to terminate the list.

• You may use either a comma (,) (C,N in the above example) or white space (C Nequivalent to above example) to separate atomic symbols that appear on the sameline.

• You may use the word rest to account for all atoms not explicitly listed; e.g., theabove example could be equivalently written as:

Basis by_element O = tz2p H = sv Cr = dz rest = dzpend_basis

The by_number option provides still greater flexibility in basis set assignment, in thatit allows you to assign a unique basis set to individual atoms, indexed by the order inwhich they are listed in the molecular geometry (see Geometry keyword, page E–43).For example, suppose the geometry of the molecule N-phenylbenzamide is enteredsuch that the atoms are numbered as in the illustration below:

C11C12

C13

C14 C15

C5

C7C6

C3

C10 C9

C8

N2

C1

O4

H16

H23 H22

H26H25

H24

H17 H18

H20H21

H19

E–14 Turbomole


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dsIf you want to use the tz2p basis set for the atoms constituting the central amide moiety(C1, N2, C3, O4, C5, H16) and the dz basis set for the rest of the molecule, you wouldwrite the Basis input as follows:

Basis by_number 1-5,16 = tz2p rest = dzend_basis

Technical Notes:

• The equal signs (=) are required separators between the integer(s) and the basis setname.

• The end_basis line is required to terminate the list.

• You may use either a comma (,) (5,16 in the above example) or white space (5 16equivalent to above example) to separate integers that appear on the same line.

• You can specify a range of atoms using a hyphen (-) (1-5 in the above example isinterpreted as atoms 1,2,3,4,5).

• You may use the word rest to account for all atoms not explicitly listed; e.g., in theabove example rest is interpreted as atoms 6-15 and 17-26.

• Symmetry is turned off for any calculation that makes use of the by_numberoption (i.e., the calculation is carried out in C1 symmetry).

A final note regarding basis set assignment: if you also want to use effective corepotentials (ECPs) for one or more atoms in your calculation (see keywords ECP, pageE–32, and ECP_Range, page E–33), the assignment of basis sets is affected. Of thetwo methods of assigning ECPs, your choice depends upon the amount of flexibilityrequired in basis set and ECP assignment. First, if you are using the Basis string modeto assign basis sets, you can assign ECPs using the ECP and ECP_Range keywords.In this case, the ECP + appropriate valence basis set is assigned to all atoms defined bythe ECP_Range keyword. The remaining atoms are “all-electron” atoms and areassigned the basis set named in string. For example, for the WF6 molecule, the input:

Basis dzpECP onECP_Range Rb-Pu

results in an ECP + valence basis set being assigned to the tungsten atom (since in peri-odic table order, W lies within the range Rb-Pu) and the dzp basis set being assignedto the six “all-electron” fluorine atoms (since in periodic table order, F does not liewithin the Rb-Pu range).

If you require greater flexibility in basis set and/or ECP assignment, you can use theby_element or by_number options of the Basis keyword. If so, you would explicitlyspecify both basis set and ECP assignments in the by_element or by_number list (theECP and ECP_Range keywords would not be used). To specify that an atom or ele-

Turbomole E–15


Comm

andsment be assigned an ECP + valence basis set using the by_element or by_number for-mat, the basis set name to use is ecp. For example, for the WF5Cl molecule, an inputof:

Basis by_element W = ecp Cl = svp F = svend_basis

results in an ECP + valence basis set being assigned to the tungsten atom, the svp basisassigned to the “all-electron” chlorine atom, and the sv basis assigned to the five “all-electron” fluorine atoms.

Note: The ECPs/valence basis sets provided in Turbomole are the averaged relativisticpseudopotentials (AREPs) of Christiansen et al. (Cundari and Stevens (1993), Ermleret al. (1991), Hurley et al. (1986), LaJohn et al. (1987), and Ross et al. (1990)) and areavailable for Li-Pu.

The Basis file string usage provides you with the option of reading basis set data fromyour own file (rather than from the Turbomole basis set library). string is used to spec-ify the name of the file from which to read the basis set data, for example:

Basis file /home/data/my_basis_sets/zeolite.basis

Your basis set file must contain a basis set entry for each atom type in your molecule(it may contain more than one basis set for a particular atom type; however, only thefirst such basis set is used—the rest are ignored). Additionally, the basis (and, ifdesired, ECP) data in your basis set file must be written in the Turbomole control fileformat. The format specifications for this file are as follows:

If you are providing basis set data only (i.e., no ECPs are desired), the file format is:

$basis<basis set 1><basis set 2><basis set 3> . . .<basis set n>*$end

If you want to include both basis set and ECP data in your basis set file, the format is:

$basis<basis set 1><basis set 2> . .

E–16 Turbomole


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ds .<basis set n>*$ecp<ECP 1><ECP 2> . . .<ECP m>*$end

Each basis set i represents a basis set entry of the following format:

The first three lines of a basis set entry constitute the basis set title.

Line 1: *Line 2: basis set aliasLine 3: *

where basis set alias is made up of an atomic symbol (in lowercase) followed by abasis set designation (which can be any valid character string).

For example, the basis set title section for a magnesium basis set with the designationdzp McLean-Chandler is written as:

*mg dzp McLean-Chandler*

Immediately following the basis set title section is the specification of the basis func-tions. Basis functions for Turbomole are assumed to be of the functional form:

Eq. E–1

For each basis function you specify

Line 4: n lLines 5-n: αi ci

where:

n = integer which defines the number of primitive functions constituting the basis func-tion

cieα ir

2–

i∑

Turbomole E–17


Comm

andsl = character defining the orbital angular momentum of the basis function (i.e., s, p, d,or f)

and αi, ci are the orbital exponents and contraction coefficients as defined in the equa-tion above.

For example, a typical basis function entry would look like

9 p663.3 -0.652145D-03156.8 -0.519445D-0249.98 -0.246938D-0118.42 -0.728167D-017.240 -0.134030D+002.922 -0.947742D-011.022 0.262289D+000.3818 0.564667D+000.13010 0.341250D+00

Lines of type 4-n are then repeated to complete the basis set.

A typical complete basis set entry would, thus, look like:

*f cc-pvdz* 9 s14710. 0.0007212207. 0.005553502.8 0.028267142.6 0.10644446.47 0.28681416.70 0.4486416.356 0.2647611.316 0.0153330.3897 -0.002332 9 s14710. -0.0001652207. -0.001308502.8 -0.006495142.6 -0.02669146.47 -0.07369016.70 -0.1707766.356 -0.1123271.316 0.5628140.3897 0.568778 1 s0.3897 1.00 4 p22.6700 0.0448784.97700 0.2357181.34700 0.508521

E–18 Turbomole


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ds0.34710 0.458120 1 p0.34710 1.00 1 d1.640 1.00

A typical user-supplied basis set file for a molecule containing the elements C, H, andCl, would look like:

$basis*h TZP huzinaga-dunning* 3 s 48.440000 0.25374000E-01 7.2840000 0.18968400 1.6520000 0.85293300 1 s0.46240000 1.0000000 1 s0.14590000 1.0000000 1 p .7500000 1.0000000*cl (13s10p)[8s6p]* 6 s 319768.12917 .14077924569E-03 47908.979619 .10935033925E-02 10902.338564 .57277566605E-02 3085.0548754 .23881295509E-01 1001.7669156 .84029783602E-01 355.77320352 .25037715237 1 s 133.89468257 1.0000000000 1 s 53.141035054 1.0000000000 1 s 22.037683418 1.0000000000 1 s 6.6684151098 1.0000000000 1 s 2.5758319044 1.0000000000 1 s .53658776971 1.0000000000 1 s .19365420149 1.0000000000 5 p 1156.9470248 .10275737954E-02 274.18526598 .85972178855E-02 88.248074269 .43148628033E-01

Turbomole E–19


Comm

ands 33.040813564 .14828111392 13.473080046 .33708191401 1 p 2.4439377447 1.0000000000 1 p 5.6972339321 1.0000000000 1 p .87616538766 1.0000000000 1 p .33316503980 1.0000000000 1 p .11861612358 1.0000000000*c tz2p hondo* 6 s 9471.0000 .77600000E-03 1398.0000 .62180000E-02 307.50000 .33575000E-01 84.540000 .13427800 26.910000 .39366800 9.4090000 .54416900 2 s 9.4090000 .24807500 3.5000000 .78284400 1 s 1.0680000 1.0000000 1 s .40020000 1.0000000 1 s .13510000 1.0000000 4 p 25.370000 .16295000E-01 5.7760000 .10209800 1.7870000 .34022800 .65770000 .66826900 1 p .24800000 1.0000000 1 p .91060000E-01 1.00 1 d .44000000 1.00 1 d 1.5800000 1.00*$end

The format for ECP entries is similar to that of basis sets. Each ECP i represents anECP entry of the following format:

E–20 Turbomole


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dsThe first three lines of a basis set entry constitute the basis set title.

Line 1: *

Line 2: ECP alias

Line 3: *

where ECP alias is made up of an atomic symbol (in lowercase) followed by an ECPdesignation (which can be any valid character string).

For example, the ECP title section for a molybdenum ECP with the designation Wadt-Hay 26 is written as;

*mo Wadt-Hay 26s*

Immediately following the ECP title section, the ECP data are specified. ECPs for Tur-bomole are assumed to be of the form:

Eq. E–2

Line 4 is used to specify the number of core electrons being replaced by the ECP andthe maximum angular momentum used in the ECP.

line 4: ncore = i1 lmax = i2

where:

i1 = integer which specifies the number of core electrons replaced by the ECP

i2 = integer which specifies the maximum angular momentum used in the ECP (s = 0,p = 1, d = 2, etc.)

The remaining lines provide the parameters for each angular momentum componentof the ECP:

line 5: lLines 6-n: ck nk αk

where:

l = character string defining the orbital angular momentum of the ECP component (i.e.,s, p, d, f, ..., or some combination thereof)

and ck, nk, αk are the contraction coefficients, radial exponents, and Gaussian expo-nents as defined in the equation above.

ck rnk

e

αkr2–

k∑

Turbomole E–21


Comm

andsFor example, a typical ECP entry would look like:

*au ecp-68-arep* ncore = 68 lmax = 4s-g -84.9692993 2 1.2248000 280.1776428 2 1.4335999 -354.6435547 2 1.8929000 334.3319092 2 2.6963000 -219.3926086 2 3.9899001 170.8587494 2 6.0054998 56.3387299 1 14.5825996 6.4092999 0 39.3106995p-g -6.9119010 2 .9064000 72.1254654 2 1.0311000 -114.9753342 2 1.3286999 123.6166840 2 1.9037000 -71.1357117 2 2.8364000 79.0166016 2 4.5883999 51.2870064 1 11.1981001 5.6519828 0 32.2957001d-g -.1136570 2 .2931000 -2.4040251 2 1.0301000 62.5811157 2 2.0186000 255.4471741 2 3.4391999 -161.8064728 2 5.1578999 -175.7707672 2 2.5149000 63.6207924 1 8.0623999 6.7503200 0 41.0284996f-g -47.6077995 2 .4335000 176.3180237 2 .5097000 -168.6768951 2 .5796000 54.4924469 2 .7711000 37.7153931 2 2.5934999 -24.1396751 2 8.3907003 49.1680222 1 6.9294000 4.7595859 0 22.2588997g -.9869020 2 .9657000 -9.6863060 2 2.2904000 -32.5724640 2 6.4383998 -118.5308762 2 16.3645992 -286.2546387 2 55.9892998 -51.2742310 1 171.1013947

E–22 Turbomole


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man

dsA typical user-supplied basis set file for a molecule containing the elements Pt, C, H,and Cl (for which the core electrons of all platinum atoms will be treated with an ECPand the carbon, hydrogen, and chlorine atoms will be treated “all-electron”) wouldlook like:

$basis*h TZP huzinaga-dunning* 3 s 48.440000 0.25374000E-01 7.2840000 0.18968400 1.6520000 0.85293300 1 s0.46240000 1.0000000 1 s0.14590000 1.0000000 1 p .7500000 1.0000000*cl (13s10p)[8s6p]* 6 s 319768.12917 .14077924569E-03 47908.979619 .10935033925E-02 10902.338564 .57277566605E-02 3085.0548754 .23881295509E-01 1001.7669156 .84029783602E-01 355.77320352 .25037715237 1 s 133.89468257 1.0000000000 1 s 53.141035054 1.0000000000 1 s 22.037683418 1.0000000000 1 s 6.6684151098 1.0000000000 1 s 2.5758319044 1.0000000000 1 s .53658776971 1.0000000000 1 s .19365420149 1.0000000000 5 p 1156.9470248 .10275737954E-02 274.18526598 .85972178855E-02 88.248074269 .43148628033E-01 33.040813564 .14828111392 13.473080046 .33708191401 1 p 2.4439377447 1.0000000000

Turbomole E–23


Comm

ands 1 p 5.6972339321 1.0000000000 1 p .87616538766 1.0000000000 1 p .33316503980 1.0000000000 1 p .11861612358 1.0000000000*c tz2p hondo* 6 s 9471.0000 .77600000E-03 1398.0000 .62180000E-02 307.50000 .33575000E-01 84.540000 .13427800 26.910000 .39366800 9.4090000 .54416900 2 s 9.4090000 .24807500 3.5000000 .78284400 1 s 1.0680000 1.0000000 1 s .40020000 1.0000000 1 s .13510000 1.0000000 4 p 25.370000 .16295000E-01 5.7760000 .10209800 1.7870000 .34022800 .65770000 .66826900 1 p .24800000 1.0000000 1 p .91060000E-01 1.00 1 d .44000000 1.00 1 d 1.5800000 1.00*pt 60-arep 4s3p3d* 2 s 2.3654 -2.6425 1.8045 3.0525 1 s 0.5083 0.4221 1 s 0.1484 -0.0196 1 s

E–24 Turbomole


Com

man

ds 0.05148 0.0064 3 p 3.3722 -0.6032 2.5328 0.6130 1.2740 0.4983 1 p 0.6238 0.4190 1 p 0.2210 0.0517 2 d 1.4463 0.2542 0.8898 0.3757 1 d 0.3387 0.4211 1 d 0.1320 0.1435*$ecp*pt ecp-60-arep* ncore = 60 lmax = 4s-g -26.6245232 2 2.6091001 90.0141220 2 3.0292001 -193.8634033 2 4.0429001 432.6285095 2 6.0763001 -343.0379333 2 9.8383999 387.9856873 2 16.7040997 29.7609482 1 47.6231003 6.7787342 0 40.0689011p-g -30.3742008 2 2.3127999 102.4953003 2 2.6817000 -205.2801514 2 3.5012000 412.8767700 2 5.1349001 -373.5076904 2 8.0056000 355.2335205 2 12.8712997 34.3938103 1 35.5367012 5.9013581 0 36.6483002d-g -3.0278800 2 1.3830000 64.2114944 2 2.0704999 -146.1029968 2 2.4905000 266.6141357 2 3.6737001 -301.4702759 2 5.4851999 278.5104370 2 8.2098999 29.7185230 1 18.5718002 7.8689160 0 25.4209995f-g -63.3894348 2 1.8671000

Turbomole E–25

Commands—Standalone Mode Basis_Type

Comm

ands 215.7241974 2 2.2018001 -333.9588013 2 2.9521000 368.0679626 2 4.3723998 -242.7938690 2 6.7848001 233.0248413 2 11.0228004 43.5935516 1 27.7359009 4.5326500 0 54.8493004g -.8125420 2 1.8648000 -13.0529289 2 4.8308001 -73.7209854 2 12.3044996 -141.1714478 2 34.8681984 -412.5782471 2 110.9464035 -52.7245255 1 378.4443054*$end

Note that each line of the basis set file is read free format (i.e., fields need not begin orend at a specific column and the amount of white space between fields is not signifi-cant), and real numbers may be entered either in standard or exponential notation (e.g.,250.0 or 0.2500E+03).

Basis_Type


auto (default)

5d/7f

6d/10f


The Basis_Type keyword is used to select the representation to use for d-type and f-type basis functions by selecting one of the options listed above, for example:

Basis auto

Where the actions of the options are:

auto:

Use 5d/7f for all basis sets except those Pople-type basis sets for which 6d/10fis the standard (i.e., 3-21G, 6-31G, 6-31G*, and 6-31G**).

E–26 Turbomole

Boys_Localization Commands—Standalone Mode

Com

man

ds5d/7f:

Use the pure 5d and 7f representations.

6d/10f:

Use the unprojected Cartesian 6d and 10f representations.

Boys_Localization


off (default)

on


The Boys_Localization keyword activates the Boys MO localization of all occupiedMOs, for example:

Boys_Localization on

The actions of the options are:

off:

No Boys localization.

on:

Activate Boys localization.

Note that the localized orbitals can be plotted for viewing in the Insight interface (seePlot keyword, page E–64).

Calculate


energy (default)

gradient

Turbomole E–27

Commands—Standalone Mode Calculate

Comm

andsoptimize

frequency

optimize_frequency

numfreq


The Calculate keyword is used to select the type of calculation to perform. You pro-vide one of the options from the above, for example:

Calculate frequency

where the actions of the options are:

energy:

Calculate molecular energy at fixed geometry.

gradient:

Calculate molecular energy + atomic forces at fixed geometry.

optimize:

Optimize molecular geometry.

frequency:

Calculate vibrational frequencies + IR intensities at fixed geometry. This typeof calculation is done analytically unless analytic 2nd derivatives are unavail-able (i.e., for MP2, for open-shell wavefunctions, and for all dft functionalsexcept VWN), in which case it is done via finite-differences-of-energy 1stderivatives.

optimize_frequency:

Optimize molecular geometry, then calculate vibrational frequencies + IR inten-sities at optimized geometry. The frequency portion of this type of calculationis done analytically unless analytic 2nd derivatives are unavailable (i.e., forMP2, for open-shell wavefunctions, and for all dft functionals except VWN), inwhich case it is done via finite-differences of energy 1st derivatives.

numfreq:

Calculate vibrational frequencies via finite-differences-of-energy 1st deriva-tives.

E–28 Turbomole

Charge Commands—Standalone Mode

Com

man

ds

Charge

Options:



The Charge keyword is used to specify the total molecular charge, e.g., for a cationicmolecule:

Charge 1

integer can be any integer.

CONSTRAINT

Options:

constraint specifications


The CONSTRAINT keyword is used to specify the distance, angle, and dihedral angleconstraints that are to be enforced during a geometry optimization. The constraintspecifications are input on separate lines of the input file (immediately following theline containing the CONSTRAINT keyword) and are specified as:

atom_i atom_j distanceatom_i atom_j atom_k angleatom_i atom_j atom_k atom_l dihedralENDCON

Where the atoms are indexed by integers in the order in which they appear in themolecular geometry, distances are expressed in angstroms, and bond angles and dihe-dral angles are expressed in degrees. The constraint specifications must be terminatedwith a separate line containing only the string ENDCON immediately following thelast constraint definition.

For example, referring to the N-phenylbenzamide geometry above (see Basis key-word, page E–10), the following CONSTRAINT input would define four constraints:the central N2-C1 amide bond distance constrained to 1.336 Å, the C5-N2-C1 angle

Turbomole E–29

Commands—Standalone Mode Constraint_Method

Comm

andsconstrained to 120.0 degrees, the H16-N2-C1-C5 dihedral angle constrained to 168.8degrees, and the C5-C3 distance constrained to 4.12 Å:

CONSTRAINT 1 2 1.336 5 2 1 120.0 16 2 1 5 168.8 5 3 4.12ENDCON

Constraint_Method


lagrange

penalty

lagrange/penalty

penalty/lagrange


The Constraint_Method keyword is used to specify the method to use for enforcinggeometric constraints for geometry optimizations in which one or more geometricaldegrees of freedom are constrained, for example:

Constraint_Method lagrange/penalty


lagrange:

Constraints are enforced using the method of Lagrange multipliers.

penalty:

Constraints are enforced using the penalty function method.

lagrange/penalty:

Constraints are enforced using the method of Lagrange multipliers, but themethod is switched to penalty functions if the Lagrange multiplier methodencounters a problem during the optimization.

E–30 Turbomole

Damping Commands—Standalone Mode

Com

man

dspenalty/lagrange:

Constraints are enforced using the penalty function method; after convergencehas been reached with penalty functions, the method is switched to that ofLagrange multipliers to tighten up the constraints.

The constraints are defined using the keywords CONSTRAINT and/or FIXED (seepage E–28 and page E–39, respectively).

Technical Notes:

• In general, the method of Lagrange multipliers is more accurate and more efficientthan the penalty functions method. However, the penalty functions method is, ingeneral, more robust. Therefore, for most cases, the recommended option for theConstraint_Method keyword is lagrange/penalty. Using this option, constraintsare handled initially using the more efficient and accurate Lagrange multipliermethod. However, if the Lagrange multiplier method encounters a problem, theoptimizer switches to the more robust (less prone to problems) penalty functionmethod. After the optimizer has reached convergence using the penalty functionmethod, the method is switched back to Lagrange multipliers to tighten up the con-straints.

• The constraints need not be satisfied at the starting geometry. However, if the con-straints are far from their constrained values at the starting geometry, several initialoptimization cycles are used to adjust the geometry so that the constraints are moreclosely satisfied. Thus it is recommended that, if possible, you start at a geometryfor which your constraints are approximately satisfied.

Damping


auto (default)

off

real


The Damping keyword is used to specify the damping factor used to damp SCF steps(which can provide smoother SCF convergence behavior), for example:

Damping 0.2

Turbomole E–31

Commands—Standalone Mode DIIS

Comm

andsThe actions of the options are:

auto:

The damping factor is set to 0.67 (0.4 for open-shell states) at the start of theSCF procedure, and, as SCF convergence is approached, the damping factor isincreased (to a maximum of 0.91).

off:

Do not damp SCF steps.

real:

Damp SCF steps by real. Note that real must lie in the range 0.0 < real <= 1.0and that a value 1.0 is equivalent to selecting the off option.

DIIS



off


The DIIS keyword is used to activate the direct inversion of the iterative subspace(DIIS) convergence acceleration procedure in the SCF, for example:

DIIS 3


integer:

Use a maximum of integer previous iterations of SCF information in the DIISextrapolation procedure.

off:

Do not use the DIIS extrapolation procedure.

E–32 Turbomole

Displacement_Convergence Commands—Standalone Mode

Com

man

ds

Displacement_Convergence

Options:

real (default = 0.0003)


The Displacement_Convergence keyword is used to specify the geometry optimiza-tion convergence criterion for the displacement vector, for example:

Displacement_Convergence 0.0003

The displacement criterion is met if the largest (in magnitude) component of the dis-placement vector is less than real. The geometry is considered optimized when the gra-dient convergence criterion (see Gradient_Convergence keyword, page E–50) issatisfied and either (or both) of the displacement convergence criterion or energy con-vergence criterion (see Opt_Energy_Convergence keyword, page E–62) is satisfied.

ECP


off (default)

on


The ECP keyword is used to activate the use of effective core potentials (ECPs) inyour calculation. The options have the following actions:

off:

Do not use ECPs.

on:

Use ECPs for all atoms specified by the ECP_Range keyword (see page E–33).The ECPs provided in Turbomole are the averaged relativistic effective poten-tials (AREPs) developed by Christiansen et al. (Cundari and Stevens (1993),Ermler et al. (1991), Hurley et al. (1986), LaJohn et al. (1987), and Ross et al.(1990)) and are available for elements Li-Pu.

Turbomole E–33

Commands—Standalone Mode ECP_Range

Comm

andsThe ECP keyword is not used if you want to provide your own ECPs (i.e., not use theECPs in the Turbomole basis set/ECP library). If so, you need to use the Basis key-word with the file string option. Refer to the Basis keyword (page E–10 ff.) for details.

ECP_Range


Li-Pu

Na-Pu

K-Pu

Rb-Pu (default)


The ECP_Range is used to specify which atoms in your molecule will make use ofeffective core potentials to represent their core electrons when the ECP keyword is setto on (see ECP keyword, page E–32). You select one of the options from the list above,for example:

ECP_Range Na-Pu


Li-Pu:

All atoms included in the range lithium-plutonium (in periodic table order)make use of ECPs.

Na-Pu:

All atoms included in the range sodium-plutonium (in periodic table order)make use of ECPs.

K-Pu:

All atoms included in the range potassium-plutonium (in periodic table order)make use of ECPs.

Rb-Pu:

All atoms included in the range rubidium-plutonium (in periodic table order)make use of ECPs.

E–34 Turbomole

Electric_Field Commands—Standalone Mode

Com

man

dsThe atoms in your molecule that do not make use of ECPs are treated with standardall-electron methodology using the basis set selected with the Basis keyword (see pageE–10). The atoms that do make use of ECPs are assigned the appropriate valence elec-tron basis set. For example, for the WF6 molecule, the input:

Basis dzpECP onECP_Range Rb-Pu

would result in an ECP + valence basis set being assigned to the tungsten atom (sincein periodic table order, W lies within the range Rb-Pu) and the dzp basis set beingassigned to the six “all-electron” fluorine atoms (since in periodic table order, F doesnot lie within the Rb-Pu range).

If you require greater flexibility in basis set and/or ECP assignment, you would use theby_element or by_number options of the Basis keyword and would explicitly specifyboth basis set and ECP assignments in the by_element or by_number list (the ECPand ECP_Range keywords would not be used). To specify that an atom or element beassigned an ECP + valence basis set using the by_element or by_number format, thebasis set name to use is ecp. For example, for the WF5Cl molecule, an input of:

Basis by_element W = ecp Cl = svp F = svend_basis

would result in an ECP + valence basis set being assigned to the tungsten atom, the svpbasis assigned to the “all-electron” chlorine atom, and the sv basis assigned to the five“all-electron” fluorine atoms.

Electric_Field


off (default)

real1 real2 real3


The Electric_Field keyword is used to include an external static electric field in yourTurbomole calculation by providing the x,y,z Cartesian components of the field, forexample:

Turbomole E–35

Commands—Standalone Mode Electrostatic_Moments

Comm

andsElectric_Field -0.383 0.0 0.255


off:

Do not include an external electric field.

real1 real2 real3:

Include the electric field defined by:

real1: x-component of field

real2: y-component of field

real3: z-component of field

The Cartesian components are in atomic units (AU); 1 AU = 5.1423*10^11 V/m

Note that Turbomole uses no symmetry when Electric_Field is active (i.e., calculationare done in C1 symmetry).

Electrostatic_Moments


off (default)

on


The Electrostatic_Moments keyword activates the calculation of the 0th (charge), 1st(dipole), 2nd, 3rd, and 4th Cartesian molecular electrostatic moments, for example:

Electrostatic_Moments on


off:

Do not calculate electrostatic moments.

on:

Activate electrostatic moments calculation.

E–36 Turbomole

ESP_Charges Commands—Standalone Mode

Com

man

ds

ESP_Charges

Options:

off (default)

on


The ESP_Charges keyword is used to activate the calculation of atomic charges, forexample:

ESP_Charges on


off:

No ESP atomic charge analysis.

on:

Calculate atomic charges based on a fit to the molecular electrostatic potential.

Note that if you want to activate more than one population analysis technique, morethan one of the Mulliken_Analysis, Loewdin_Analysis, Roby_Davidson_Analysis,and ESP_Charges keywords may be specified as on.

Excitation_Energy


off (default)

on


The Excitation_Energy keyword activates the calculation of excited-state transitionenergies and transition oscillator strengths, for example:

Excitation_Energy on

Turbomole E–37

Commands—Standalone Mode Excited_State_Method

Comm


off:

Do not calculate excited state energies/oscillator strengths.

on:

Activate excited state energy/oscillator strength calculation; you will need toprovide details of the excited state calculation via the keywords Excited_State_Method (page E–37), Excited_State_Symmetry (page E–38), Excited_State_Multiplicity (page E–38), and Number_Of_Excited_States (page E–61).



sci (default)

rpa


The Excited_State_Method keyword is used to select the method by which to per-form the calculation of excited-state transition energies and oscillator strengths (seealso Excitation_Energy keyword, page E–36), for example:

Excited_State_Method rpa


sci:

Use the singles CI method for the excitation energy calculation.

rpa:

Use the random phase approximation method for the excitation energy calcula-tion.

Technical Note: the rpa method is typically a more accurate, but more time-consum-ing, calculation than sci.

E–38 Turbomole

Excited_State_Multiplicity Commands—Standalone Mode

Com

man

ds

Excited_State_Multiplicity


singlet (default)

triplet


The Excited_State_Multiplicity keyword is used to select the spin multiplicity of theexcited-state wavefunction for which to perform the calculation of excited-state tran-sition energies and oscillator strengths (see also Excitation_Energy keyword, page E–36), for example:

Excited_State_Multiplicity singlet


singlet:

Perform the excitation energy calculation for spin singlet excited states.

triplet:

Perform the excitation energy calculation for spin triplet excited states.

Excited_State_Symmetry


default (default)

string


The Excited_State_Symmetry keyword is used to specify the spatial symmetry of theexcited-state wavefunction for which to perform the calculation of excited-state tran-sition energies and oscillator strengths (see also Excitation_Energy keyword, page E–36), for example:

Excited_State_Symmetry b2

Turbomole E–39

Commands—Standalone Mode FIXED

Comm


default:

Perform the excitation energy calculation for excited states that transformaccording to the totally symmetric irreducible representation of the point group(e.g., A1 states for a molecule having C2v symmetry).

string:

Perform the excitation energy calculation for excited states that transformaccording to the irreducible representation specified in string. The exampleshown above would, thus, result in calculations on excited B2 states.

FIXED

Options:

fix coordinate specifications


The FIXED keyword is used to specify Cartesian constraints (i.e., to constrain the xand/or y and/or z coordinate(s) of specified atom(s)) that are to be enforced during ageometry optimization. The fix coordinate specifications are input on separate lines ofthe input file (immediately following the line containing the FIXED keyword) and arespecified as:

atom x (and/or) y (and/or) z

Where the atoms are indexed by integers in the order in which they appear in themolecular geometry. The fix coordinate specifications must be terminated with a sep-arate line containing only the string endfix immediately following the last fixed atomdefinition.

For example, referring to the N-phenylbenzamide geometry above (see Basis key-word, page E–10), the following Fixed input would define three Cartesian constraints:the y and z coordinates of N2, the x coordinate of C8, and the x, y, and z coordinatesof H16:

E–40 Turbomole

Freq_Dep_Polarizability Commands—Standalone Mode

Com

man

ds



off (default)

on


The Freq_Dep_Polarizability keyword activates the calculation of frequency-depen-dent molecular polarizability tensor(s), for example:

Freq_Dep_Polarizability on


off:

Do not calculate frequency-dependent polarizability.

on:

Activate frequency-dependent polarizability calculation. The frequency(ies) atwhich the calculation is done are specified with the Frequencies keyword (seepage E–40).

Frequencies

Options:

real(s) (default = 0.6491 1.17)


The Frequencies keyword is used to specify the frequency(ies) at which to carry outfrequency-dependent polarizability calculation (see also Freq_Dep_Polarizabilitykeyword, page E–40), for example:

Frequencies 2.66 1.24 0.995

Turbomole E–41

Commands—Standalone Mode Functionals

Comm


real(s):

Calculate the frequency-dependent polarizability tensor for each frequencyspecified by each real (in units of eV).

Functionals


ACM

B88

BLYP

BP

BVWN

SLATER

SVWN (default)


The Functionals keyword is used to select the density functionals to use for DFT cal-culations (see Method keyword, page E–57), for example:

Functionals BP


ACM:

Use the adiabatic connection method (hybrid Hartree-Fock/DFT). Selecting thisoption is an equivalent alternative to setting Method to ACM (see Method key-word, page E–57; see also ACM_Coeffs, page E–8).

B88:

Use a functional composed of the Becke-88 non-local exchange only (no corre-lation functional is used).

E–42 Turbomole

GDIIS Commands—Standalone Mode

Com

man

dsBLYP:

Use a functional composed of the Becke-88 non-local exchange + the Lee YangParr non-local correlation.

BP:

Use a functional composed of the Becke-88 non-local exchange + the PerdewWang non-local correlation.

BVWN:

Use a functional composed of the Becke-88 non-local exchange + the VoskoWilk Nusair local correlation.

SLATER:

Use a functional composed of the Slater local exchange only (no correlationfunctional is used).

SVWN:

Use a functional composed of the Slater local exchange + the Vosko WilkNusair local correlation

GDIIS


off (default)

auto

integer


The GDIIS keyword is used to select the DIIS convergence procedure for geometryoptimization, for example:

GDIIS auto


off:

Do not use the GDIIS procedure.

Turbomole E–43

Commands—Standalone Mode Geometry

Comm

andsauto:

Turbomole automatically determines the maximum number of steps from whichto use information for the GDIIS procedure.

integer:

Use the information from a maximum of integer optimization steps for theGDIIS procedure.

Note: GDIIS can be used only for optimizations to minima. Transition-state searchesmust be done with GDIIS off.

Geometry


car (default)

xyz

zmat

Where the car and xyz options have these suboptions:

ang (default)

bohr

And the syntaxes of the xyz and zmat options are:

xyz atomic_symbol_1 x1 y1 z1 atomic_symbol_2 x2 y2 z2 ... . . .end_geom

zmat z-matrixend_geom


The Geometry keyword is used to provide the molecular geometry for your Turbo-mole calculation. You provide one of the options, and, if desired, one of the suboptionsfrom the lists above, for example:

E–44 Turbomole

Geometry Commands—Standalone Mode

Com

man

dsGeometry zmat C1 C2 C1 rCC H3 C1 rCH C2 a H4 C1 rCH C2 a H3 180. H5 C2 rCH C1 a H2 0. H6 C2 rCH C1 a H2 180. rCC 1.375 rCH 1.075 a 123.end_geom

where the usage of each of the options and suboptions is described below.

With the car option, Turbomole reads the geometry from your run_name.car file. Theang or bohr suboptions are used to indicate the units (either angstroms or Bohrs,respectively) in which your .car file is written. For example, if you executed the tur-bomole script as:

> turbomole alcl3

and your alcl3.input file contained Geometry input as:

Geometry car ang

The molecular geometry is read (in angstroms) from the file alcl3.car (which mustreside in the directory from which you launched your job). In addition, if the alcl3.mdffile exists in this same directory, the molecular connectivity information is read fromit (however, an .mdf file need not exist). Please refer to the File Formats documentationfor a description and examples of Biosym .car and .mdf file formats.

With the xyz option, you can enter Cartesian coordinates directly in the input file. Forexample, xyz input for HCN in units of Bohr, could be written as:

Geometry xyz bohr C 0.0 0.0 -0.063 N 0.0 0.0 2.129 H 0.0 0.0 2.066end_geom

Note: the end_geom line is required as the terminator for xyz input.

With the zmat option, you can enter the molecular geometry in z-matrix form directlyin the input file. The z-matrix (which has traditionally been a popular scheme for input-ting geometry into standalone molecular quantum chemistry programs) enables you toexpress the geometry in terms of bond distances, bond angles, and dihedral angles (i.e.,simple internal coordinates). The format for generic z-matrix lines is:

line 1: E line 2: E N1 L line 3: E N1 L N2 Alines 4-n: E N1 L N2 A N3 D

Turbomole E–45


Comm

andswhere:

E is the element symbol of the new atom;

N1 is the number of a previously defined atom;

L is the distance between E and N1;

N2 is another previously defined atom;

A is the angle (in degrees) defined by E-N1-N2 (with N1 residing at the apex);

N3 is yet another previously defined atom;

D is the dihedral angle (in degrees) between the E-N1-N2 and N1-N2-N3 planes.Note that the dihedral (or torsion) angle is defined over the interval -180 < D <=180 and has a positive sign if, when viewing the atoms along the bond N1-N2 withN1 nearer the viewer than N2, the angle from the projection of E-N1 to the projec-tion of N2-N3 is traced in the clockwise sense. This sign convention is illustratedwith the following Newman projections, in which the E-N1-N2-N3 dihedral angleis > 0 in the example on the left and < 0 in the example on the right.

For example, the geometry of the hydrogen peroxide molecule:

could be input using the above z-matrix format as follows:

Geometry zmat O O 1 1.2 H 1 1.0 2 120.0 H 2 1.0 1 120.0 3 110.0end_geom

N1

N3

E

I (D > 0)

N1

N3

E

II (D < 0)

H3

O1 O2

H4

E–46 Turbomole


Com

man

dsline 1 defines an O as atom 1;

line 2 defines another O as atom 2 with a 2-1 (O-O) distance of 1.2 angstroms;

line 3 defines an H as atom 3 with a 3-1 (O-H) distance of 1.0 angstrom and a 3-1-2 (H-O-O) angle of 120.0 degrees

line 4 defines another H as atom 4 with a 4-2 (H-O) distance 1.0 angstrom, a 4-2-1(H-O-O) angle of 120.0 degrees, and a 4-2-1-3 (H-O-O-H) dihedral angle of 110.0degrees;

The end_geom line is required as the terminator for zmat input.

There are several variants of the basic z-matrix format described above, which can alsobe used. One variant is to use the element symbol (E) for defining connectivity ratherthan integers (N). For example, a z-matrix for the PbFClBrI molecule:

could be written as:

Geometry zmat Pb F Pb 2.054 Cl Pb 2.460 F 107.07 Br Pb 2.631 F 107.39 Cl -117.50 I Pb 2.815 F 109.45 Cl 121.01end_geom

Additionally, the element symbols (E) can be extended (up to a total of six characters)to allow atoms with the same atomic symbol to be distinguished from one anotherwithin the z-matrix. For example, using the hydrogen peroxide molecule illustratedabove, the z-matrix can be written such that the two oxygens and two hydrogens haveunique element symbols and can thus be distinguished:

Geometry zmat O1 O2 O1 1.2 Ha O1 1.0 O2 120.0 Hb O2 1.0 O1 120.0 Ha 110.0end_geom

Such a z-matrix generates exactly the same molecular geometry as the one defined pre-viously, but can be much simpler for a human to read and interpret (particularly formolecules containing a relatively large number of atoms) than a z-matrix in which inte-

Pb1

Br4

I5

F2

Cl3

Turbomole E–47


Comm

andsgers are used to define the connectivity as done in the first HOOH z-matrix writtenabove.

Note that the first two characters of each element symbol (E) are parsed to determinethe atom type. Thus, if you modified the hydrogen peroxide z-matrix to read:

Geometry zmat Oh_Boy OShux Oh_Boy 1.2 Hank Oh_Boy 1.0 OShux 120.0 Henry OShux 1.0 Oh_Boy 120.0 Hank 110.0end_geom

you would not generate an HOOH molecule. The first and third atoms would be inter-preted as intended (i.e., as oxygen and hydrogen, respectively), but the second atomwould be read as osmium and the fourth as helium.

Another variation in the z-matrix format is to use parameter names to represent bonddistances, bond angles, and dihedral angles (rather than entering the values directly inthe z-matrix). In such a format, values for each of the parameters are assigned imme-diately following the z-matrix (with the z-matrix section and the parameter assignmentsection separated by one blank line). For example, the hydrogen peroxide z-matrixcould be written:

Geometry zmat O1 O2 O1 rOO H1 O1 rOH O2 a H2 O2 rOH O1 a H1 d rOO 1.2 rOH 1.0 a 120.0 d 110.0end_geom

This z-matrix would generate the same geometry as the HOOH z-matrices writtenabove. Here the string “rOO” is used as the parameter name representing the O-O dis-tance, and similarly, “rOH” for the two O-H distances, “a” for the two HOO angles,and “d” for the HOOH dihedral angle. The z-matrix is followed by one blank line, andon the final four lines, values are assigned to the four parameters.

Both parameters and direct input of values can be used within the same z-matrix. Forexample, a z-matrix for acetone:

E–48 Turbomole


Com

man

ds

could be written as:

Geometry zmat C1 O2 C1 r1 C3 C1 r2 O2 a1 C4 C1 r2 O2 a1 C3 180.0 H5 C3 r3 C1 a2 O2 0.0 H6 C3 r4 C1 a3 H5 d1 H7 C3 r4 C1 a3 H5 -d1 H8 C4 r3 C1 a2 O2 0.0 H9 C4 r4 C1 a3 H8 d1 H10 C4 r4 C1 a3 H8 -d1 r1 1.23 r2 1.51 r3 1.10 r4 1.09 a1 119.7 a2 110.8 a3 110.8 d1 119.9end_geom

Note the use of d1 and -d1 to assign dihedral angles (of the same value but oppositesign) to the out-of-plane methyl group hydrogens.

The final variation that can be used in z-matrix construction is that of dummy atoms.Dummy atoms are used in defining the geometry of a molecule, but are not actuallyatoms belonging to the molecule: they are simply positions that are defined relative tothe atoms of the molecule because they are helpful in constructing a z-matrix for themolecule. Dummy atoms are represented by symbols “X” or “Q” in a z-matrix.

There is one situation where dummy atoms must be employed: if a fourth atom isadded to three co-linear atoms, then the dihedral angle needed to position the fourthatom cannot be defined. The remedy in this situation is to add a dummy atom anddefine the new (fourth) atom and its dihedral angle with respect to the dummy atom,for example, for the allene molecule:

H5

C3

C1

C4

O2H10

H9

H8

H7

H6

Turbomole E–49


Comm

ands

Geometry zmat C1 X C1 1.0 C2 C1 r1 X 90.0 C3 C1 r1 X 90.0 C2 180.0 H4 C2 r2 C1 a X 90.0 H5 C2 r2 C1 a X -90.0 H6 C3 r2 C1 a X 0.0 H7 C3 r2 C1 a X 180.0 r1 1.335 r2 1.084 a 118.3end_geom

Dummy atoms are often used to help construct z-matrices for rings and other linkedstructures, particularly when parameters are identical due to symmetry, for example,for benzene:

Geometry zmat X C1 X r1 C2 X r1 C1 60.0 C3 X r1 C2 60.0 C1 180.0 C4 X r1 C3 60.0 C2 180.0 C5 X r1 C4 60.0 C3 180.0 C6 X r1 C5 60.0 C4 180.0 H7 C1 r2 C2 120.0 X 180.0 H8 C2 r2 C3 120.0 X 180.0 H9 C3 r2 C4 120.0 X 180.0 H10 C4 r2 C5 130.0 X 180.0

x

C1

H6

H7

H4

H5

C2 C3

xC1

C6 C5

C4

C3C2

H7

H12 H11

H10

H9H8

E–50 Turbomole

Gradient_Convergence Commands—Standalone Mode

Com

man

ds H11 C5 r2 C6 120.0 X 180.0 H12 C6 r2 C1 120.0 X 180.0 r1 1.395 r2 1.077end_geom

One final note regarding z-matrix input. In Turbomole 95.0/3.00, the z-matrix is usedsolely as a means of inputting the molecular geometry. The z-matrix coordinates areimmediately converted to Cartesian coordinates. The symmetry of the molecule isdetermined from the Cartesian coordinates and not from the z-matrix. Additionally,geometry optimization is carried out either in the Cartesian coordinates or in a set ofnatural internal coordinates automatically determined by Turbomole (see Opt_Coordinate_System keyword, page E–61)—not using the z-matrix parameters asoptimization coordinates. Consequently, there is no necessity to ensure that the numberof parameters in the z-matrix corresponds to the number of degrees of freedom (includ-ing symmetry) that your molecule actually possesses.

Note also that, for jobs in which the geometry was not provided from a .car file (i.e.,either the xyz or zmat option was used), a .car file will be created based on the originalxyz or zmat input. Any updates to the geometry (e.g., during a geometry optimization)are written to the .car file. Thus, the original geometry written in your input file isunchanged.

Gradient_Convergence

Options:



The Gradient_Convergence keyword is used to specify the geometry optimizationconvergence criterion for the gradient vector, for example:

Gradient_Convergence 0.0004

The gradient criterion is met if the largest (in magnitude) component of the gradientvector is less than real. The geometry is considered optimized when the gradient con-vergence criterion is satisfied and either (or both) of the displacement convergence cri-terion or energy convergence criterion is satisfied (see Displacement_Convergence,page E–32) and Opt_Energy_Convergence (page E–62) keywords).

Turbomole E–51

Commands—Standalone Mode Grid

Comm

ands

Grid

Options (specify all):

grid1 points Nx range xmin xmax

grid2 points Ny range ymin ymax

grid3 points Nz range zmin zmax


The Grid keyword is used to define the 3D rectangular region for plotting the dataspecified using the Plot keyword (see page E–64). The Grid keyword is entered on itsown line in your input file and immediately followed by three additional lines thatdefine the 3D rectangular grid, for example:

Gridgrid1 points 50 range -6.50 6.50grid2 points 70 range -20.22 18.745grid3 points 35 range -0.825 4.33

The grid is defined using three integer values:

Nx:

Total number of uniformly-spaced points along the x-dimension of the grid.

Ny:

Total number of uniformly-spaced points along the y-dimension of the grid.

Nz:

Total number of uniformly-spaced points along the z-dimension of the grid andthree pairs of real values:

xmin xmax:

Lower and upper bounds of grid in the x-dimension.

ymin ymax:

Lower and upper bounds of grid in the y-dimension.

zmin zmax:

Lower and upper bounds of grid in the z-dimension.

E–52 Turbomole

Hessian_File Commands—Standalone Mode

Com

man

ds

Hessian_File


none (default)

string


The Hessian_File keyword is used for reading the starting Hessian matrix for thegeometry optimization from a file, for example:

Hessian_File ../archive/ch3nh2.hessian


none:

No file is read; a default diagonal starting Hessian matrix is supplied by the opti-mizer.

string:

Read starting Hessian matrix from file string. The file must contain Hessianmatrix in Biosym/MSI .hessian file format (see File Formats book).

Hessian_Update


Powell (default for transition-state optimizations)

BFGS (default for minimizations with GDIIS off)

BFGS_safe (default for minimizations with GDIIS on)

none


The Hessian_Update keyword is used to select the method for updating the Hessianmatrix during the course of the geometry optimization, for example:

Turbomole E–53

Commands—Standalone Mode Integration_Grid

Comm

andsHessian_Update BFGS


Powell:

Use the Powell Hessian update method.

BFGS:

Use the Broyden-Fletcher-Goldfarb-Shanno Hessian update method.

BFGS_safe:

Use a modified BFGS method with safeguards to ensure the Hessian remainspositive definite.

none:

Do not update the Hessian matrix.

Integration_Grid


xfine

fine

medium (default)

coarse

xcoarse


The Integration_Grid keyword is used to specify the grid quality over which to carryout the DFT numerical integration. For example, to specify that a fine grid be used foryour DFT calculation, you would include the following line in your input file:

Integration_Grid fine

The total numbers of grid points per atom for each of the grid sizes are listed in thefollowing table (for the first three rows of the periodic table only—the numbers of gridpoints for the heavier elements depend on how ECPs are used):

E–54 Turbomole

Level_Shift Commands—Standalone Mode

Com

man

ds

Note that both the numerical accuracy and the CPU cost of the DFT calculationincrease as the grid is made larger. For most calculations, the default (medium) gridprovides sufficient numerical accuracy for DFT energies, forces, geometries, and fre-quencies.

Level_Shift

Options:


off


The Level_Shift keyword is used to activate automatic energy level shifting of virtualorbitals during the SCF procedure to improve SCF convergence when the gap betweenthe occupied and virtual MOs is small, for example:

Level_Shift 0.25


real:

Automatically shift virtual orbitals to a higher energy when the HOMO-LUMOgap is less than real au.

off:

Do not shift the virtual orbitals.

Table E–2. Grid points per atom

H, He 1st-row 2nd-row 3rd-row

xfine 13800 29000 30700 33300fine 7500 11500 12900 13800medium 3300 5900 6600 7500coarse 1700 3300 3900 4400xcoarse 800 1700 2000 2400

Turbomole E–55

Commands—Standalone Mode Locate

Comm

ands

Locate


minimum (default)

transition_state


The Locate keyword is used to select what type of stationary point to locate during thegeometry optimization, for example:

Locate minimum


minimum:

Geometry optimizer will search for a minimum on the molecular potentialenergy surface (i.e., a stationary point at which all eigenvalues of the Hessianmatrix are > 0).

transition_state:

Geometry optimizer will search for a transition state on the molecular potentialenergy surface (i.e., a stationary point at which one and only one eigenvalue ofthe Hessian matrix is < 0).

Loewdin_Analysis

Options:

off (default)

on


The Loewdin_Analysis keyword is used to activate the Loewdin population analysisprocedure, for example:

Loewdin_Analysis on

E–56 Turbomole

Max_Core_Memory Commands—Standalone Mode

Com

man

dsThe actions of the options are:

off:

No Loewdin population analysis.

on:

Perform a Loewdin population analysis.


Max_Core_Memory

Options:



The Max_Core_Memory keyword is used to specify the amount of core memory (inMBytes) to use for holding A-matrix elements during the solution of the CPHF equa-tion (needed in both SCF frequency and MP2 calculations). For example, to allocate36 MBytes of core memory for holding A-matrix elements, you would input:

Max_Core_Memory 36

Note that you must provide core memory for A-matrix storage (i.e., integer must be >0).

Max_Displacement

Options:



The Max_Displacement keyword is used to specify the maximum length of the geom-etry update vector (in Bohrs), for example:

Turbomole E–57

Commands—Standalone Mode Method

Comm

andsMax_Displacement 0.2


real:

Maximum allowed length of the geometry update vector; if the displacementwould be larger than real, the step is scaled.

Method


ACM

DFT

HF (default)

MP2


The Method keyword is used to select the computational method to use. You provideone of the options from to list above, for example:

Method MP2

where the actions of the options are:

ACM:

Use the adiabatic connection method (hybrid DFT/Hartree-Fock) (see alsoACM_Coeffs keyword, page E–8).

DFT:

Use one of the density functional methods (see also Functionals keyword, pageE–41).

HF:

Use the Hartree-Fock method.

MP2:

Use 2nd-order Moller-Plesset perturbation theory.

E–58 Turbomole

MO_Guess Commands—Standalone Mode

Com

man

ds

MO_Guess


huckel (default)

core

string


The MO_Guess keyword is used to specify the starting SCF orbitals to use for yourcalculation by selecting one of the options from the list above, for example:

MO_Guess huckel


huckel:

Generate starting MOs from an extended-Hückel type (EHT) calculation.

core:

Use core Hamiltonian starting MOs.

string:

Read starting MOs from the file named string (typically, this would be a .turbo_archive file from a previous Turbomole calculation). The file must contain theMOs and basis set in Turbomole .turbo_archive (control file) format (see sample.turbo_archive file in Appendix C). The MOs being read need not have been cal-culated using the same basis set as that of the present calculation. A projectionis done to map the orbitals from the previous basis set onto the current basis set.


Options:


Turbomole E–59

Commands—Standalone Mode Mulliken_Analysis

Comm

andsDescription and Example

The MO_Integral_Filesize keyword is used to specify the amount of disk space (inMBytes) to use for storing MO two-electron integrals (and other two-electron/four-index quantities) for SCF frequency and MP2 calculations, e.g., to use 72 MBytes ofdisk space to store MO two-electron/4-index quantities you would input:

MO_Integral_Filesize 72

Note that, unlike the AO_Integral_Filesize keyword, you must specify an integer thatis > 0 for MO_Integral_Filesize (i.e., there is currently no fully direct SCF frequencyor MP2 capability in Turbomole). Furthermore, for any particular SCF frequency orMP2 calculation, there is a minimum value of integer, below which the calculation isnot possible (the larger the molecule/basis set, the larger this minimum becomes). Ifyou encounter such a situation, you will need to adjust the value of integer so that it is>= the minimum and re-run your calculation.

Mulliken_Analysis

Options:

off (default)

on


The Mulliken_Analysis keyword is used to activate the Mulliken population analysisprocedure, for example:

Mulliken_Analysis on


off:

No Mulliken population analysis.

on:

Perform a Mulliken population analysis.


E–60 Turbomole

Multiplicity Commands—Standalone Mode

Com

man

ds

Multiplicity

Options:

positive integer


The Multiplicity keyword is used to specify the spin multiplicity of your wavefunc-tion, e.g., for a spin triplet:

Multiplicity 3

positive integer must be > 0.

NMR_Shielding


off (default)

on


The NMR_Shielding keyword activates the calculation of a magnetic shielding tensorfor each symmetry-unique nucleus in your molecule, for example:

NMR_Shielding on


off:

Do not calculate magnetic shielding tensors.

on:

Activate magnetic shielding calculation.

Turbomole E–61

Commands—Standalone Mode Number_Of_Excited_States

Comm

ands

Number_Of_Excited_States

Options:



The Number_Of_Excited_States keyword is used to specify the number of excitedstates (defined by the Excited_State_Symmetry, page E–38, and Excited_State_Multiplicity, page E–38, keywords) to calculate (see also Excitation_Energy key-word, page E–36), for example:

Number_Of_Excited_States 6


integer:

Perform excitation energy calculation for the integer lowest energy excitedstates of the spatial symmetry defined by Excited_State_Symmetry (see pageE–38) and the spin multiplicity defined by Excited_State_Multiplicity (seepage E–38).

Opt_Coordinate_System


auto (default)

internal

cartesian


The Opt_Coordinate_System keyword is used to select the coordinate system inwhich to carry out the geometry optimization, for example:

Opt_Coordinate_System internal

E–62 Turbomole

Opt_Cycles Commands—Standalone Mode

Com

man

dsThe actions of the options are:

auto:

Attempt to optimize in natural internal coordinates; however, if a problem ariseswith the internal coordinate set (e.g., topology too complex to construct naturalinternal coordinate set, or non-convergent internal to Cartesian transformation)Turbomole automatically switches to Cartesian coordinates and continues withthe geometry optimization.

internal:

Carry out the optimization in a set of natural internal coordinates (automaticallydetermined by the Turbomole based on the topology of the molecule).

cartesian:

Carry out the optimization in Cartesian coordinates.

Opt_Cycles

Options:



The Opt_Cycles keyword is used to specify the maximum number of optimizationcycles to carry out, for example:

Opt_Cycles 80

If the geometry optimization has not converged after the completion of integer cycles,the optimization (and, thus, your Turbomole job) aborts.

Opt_Energy_Convergence

Options:


Turbomole E–63

Commands—Standalone Mode Opt_Use_Symmetry

Comm


The Opt_Energy_Convergence keyword is used to specify the geometry optimiza-tion convergence criterion for the total molecular energy, for example:

Opt_Energy_Convergence 0.00000025

The energy criterion is met if the difference between the total energy in two consecu-tive optimization steps is less than real. The geometry is considered optimized whenthe gradient convergence criterion (see Gradient_Convergence keyword, page E–50)is satisfied and either (or both) of the displacement convergence criterion (seeDisplacement_Convergence keyword, page E–32) or energy convergence criterion issatisfied.

Opt_Use_Symmetry


on (default)

off


The Opt_Use_Symmetry keyword is used to select whether molecular symmetry willbe used in the context of the geometry optimization, for example:

Opt_Use_Symmetry on


on:

All quantities used by the optimizer (Hessian matrix, geometry update vector,etc.) will be restricted to the symmetry of the molecule. Thus, the molecule willmaintain its initial symmetry throughout the optimization.

off:

Symmetry will not be enforced by the optimizer.

E–64 Turbomole

Plot Commands—Standalone Mode

Com

man

ds

Plot

Options (select one or more):

off (default)

density

potential

homo

lumo

local_homo

orbital integer(s)

local_orbital integer(s)


The Plot keyword is used to activate the generation of 3D grid(s) of data which arewritten to Biosym/MSI .grd file(s) for subsequent viewing in the Insight interface, forexample:

Plot density potential lumo

The Grid keyword (see page E–51) is also required. The actions of the options are:

off:

No 3D data plotted.

density:

Calculate and write 3D total electron density data to run_name_DENS.grd file.

potential:

Calculate and write 3D molecular electrostatic potential data to run_name_POT.grd file.

homo:

Calculate and write 3D highest occupied molecular orbital (HOMO) data torun_name_HOMO.grd file.

Turbomole E–65

Commands—Standalone Mode Plot

Comm

andslumo:

Calculate and write 3D lowest unoccupied molecular orbital (LUMO) data torun_name_LUMO.grd file.

local_homo:

Calculate and write 3D localized HOMO data to run_name_LOCAL_HOMO.grd file; (Boys_Localization keyword (see page E–26) must also beactive).

orbital integer(s):

Calculate and write 3D data for specific MOs (specified by integer(s) where 1= lowest energy MO, 2 = 2nd lowest energy MO, etc.) to run_name_MO_inte-ger(s).grd file(s).

local_orbital integer(s):

Calculate and write 3D data for specific localized occupied MOs (specified byinteger(s) where 1 = lowest energy MO, 2 = 2nd lowest energy MO, etc.) torun_name_LOCAL_MO_integer(s).grd file(s); (Boys_Localization keyword(see page E–26) must also be active).

Technical Notes:

• You can activate more than one option of the Plot keyword, e.g., to generate .grdfiles for the electrostatic potential and HOMO you would include the following linein your input file:

Plot potential homo

However, if you want to use the orbital and/or local_orbital options in combina-tion with other y options, the orbital and/or local_orbital options must appear onseparate lines (along with the Plot keyword). For example, to generate .grd files forthe HOMO, the localized HOMO, the 4th, 6th, and 9th lowest energy MOs, and thelocalized 6th lowest energy MO, you would include the following lines in yourinput file (in no particular order):

Boys_Localization onPlot homo local_homoPlot orbital 4 6 9Plot local_orbital 6

• If an orbital selected for plotting (via either homo, lumo, local_homo, orbital, orlocal_orbital) is strictly degenerate (by symmetry), separate .grd files are createdfor each member of the degenerate set. For purposes of orbital counting, an n-folddegenerate set of orbitals is counted as n orbitals (not 1 orbital). Thus, in the orbitalenergy/occupation diagram illustrated below, choosing:

E–66 Turbomole

Point_Charges Commands—Standalone Mode

Com

man

dsPlot orbital 5

or

Plot orbital 6

or

Plot orbital 7

or

Plot homo

would generate the same three .grd files for the triply degenerate orbitals 5, 6, and 7.

Point_Charges


off (default)

string


The Point_Charges keyword is used to include external point charges in your Turbo-mole calculation by providing the name of a file in which the positions and values ofthe point charges are defined, for example:

Point_Charges charge_file

1

2

3 4

5 6 7

8 9

Turbomole E–67

Commands—Standalone Mode Point_Charges

Comm


off:

Do not include any point charges in the calculation.

string:

Include point charges in the calculation as read from the file named string. Thefile must be in one of the following three formats:

Format 1:

Biosym/MSI .car file format.

Format 2:

@PCHARGESnx1 y1 z1 q1x2 y2 z2 q2. . . .xn yn zn qn

Where:

n = number of charges

xi,yi,zi = Cartesian coordinates of point charge i (in angstroms)

qi = value of point charge i (in atomic units (au); 1 au = 1.6022*10^-19 Coulomb)

Format 3:

@Point_Chargesx1 y1 z1 q1x2 y2 z2 q2. . . .xn yn zn qn

Where:

xi,yi,zi = Cartesian coordinates of point charge i (in angstroms)

qi = value of point charge i (in atomic units (AU); 1 AU = 1.6022*10^-19 Cou-lomb)

Note that Turbomole uses no symmetry when Point_Charges is active (i.e., calcula-tion is done in C1 symmetry).

E–68 Turbomole

Product Commands—Standalone Mode

Com

man

ds

Product


DMol

Turbomole

Zindo


The Product keyword is used to identify which of the Biosym/MSI quantum productsis being run, for example:

Product Turbomole

Relativistic_Correction


off (default)

on


The Relativistic_Correction keyword activates the calculation of the Cowan-Griffinrelativistic correction to the SCF energy, for example:

Relativistic_Correction on


off:

Do not calculate Cowan-Griffin relativistic correction.

on:

Activate calculation of Cowan-Griffin relativistic correction.

Turbomole E–69

Commands—Standalone Mode Roby_Davidson_Analysis

Comm

ands

Roby_Davidson_Analysis

Options:

off (default)

on


The Roby_Davidson_Analysis keyword is used to activate the Roby–Davidson pop-ulation analysis procedure, for example:

Roby_Davidson_Analysis on


off:

No Roby–Davidson population analysis.

on:

Perform a Roby–Davidson population analysis based on occupation numbers.



Options:

real (default = 10-5)


The SCF_Density_Convergence keyword is used to specify the electron density con-vergence threshold for the SCF procedure, for example:

SCF_Density_Convergence 0.00001

The SCF electron density is considered converged when the difference between thenorm of the density matrices from two successive SCF iterations is less than real. Note

E–70 Turbomole

SCF_Energy_Convergence Commands—Standalone Mode

Com

man

dsthat both the energy (see SCF_Energy_Convergence keyword, page E–70) and den-sity convergence criteria must be simultaneously satisfied for SCF convergence to beachieved.

SCF_Energy_Convergence

Options:

real (default = 10-7)


The SCF_Energy_Convergence keyword is used to specify the energy convergencethreshold for the SCF procedure, for example:

SCF_Energy_Convergence 0.0000001

The SCF energy is considered converged when the energy difference between two suc-cessive SCF iterations is less than real. Note that both the energy and density (seeSCF_Density_Convergence keyword, page E–69) convergence criteria must besimultaneously satisfied for SCF convergence to be achieved.

SCF_Iterations

Options:



The SCF_Iterations keyword is used to specify the maximum number of SCF itera-tions to carry out, for example:

SCF_Iterations 80

If the SCF procedure has not converged after the completion of integer iterations, theSCF procedure (and, thus, your Turbomole job) aborts.

Turbomole E–71

Commands—Standalone Mode Spin

Comm

ands

Spin


restricted (default)

restricted_open

unrestricted


The Spin keyword is used to specify the type of method to be used for the spin portionof the electronic wavefunction, by selecting one of the options listed above, for exam-ple:

Spin unrestricted


restricted:

Constructs a spin wavefunction for a closed-shell spin state with a necessarilyeven (2n) number of electrons paired off into the n lowest-energy molecularorbitals. Note that the restricted option necessarily implies a spin multiplicityof 1 (see Multiplicity keyword, page E–60).

restricted_open:

Constructs a spin wavefunction for an open-shell spin state in which each“closed-shell” orbital (i.e., each orbital that is fully occupied) is restricted to bespatially identical for spin-up (alpha) and spin-down (beta) electrons. This typeof open-shell wavefunction is guaranteed to be a proper eigenfunction of thetotal spin operator, S2.

unrestricted:

Constructs a spin wavefunction for an open-shell spin state in which two spa-tially distinct sets of molecular orbitals are used: “alpha” orbitals for spin-upelectrons and “beta” orbitals for spin-down electrons. This type of open-shellwavefunction is, in general, not a proper eigenfunction of the total spin operator,S2, (it suffers from so-called spin contamination); however, it has greater flexi-bility than the restricted open-shell wavefunction (e.g., for the study of bond-breaking).

Turbomole automatically generates the aufbau occupation scheme: It occupies themolecular orbitals, beginning with those having the lowest energy and proceedingupwards in energy until all the electrons have been used in a way consistent with the

E–72 Turbomole

Static_Polarizability Commands—Standalone Mode

Com

man

dsspecified charge and multiplicity (see Charge, page E–28, and Multiplicity, page E–60, keywords). However, if orbital degeneracy prevents Turbomole from determininga unique choice of orbital occupation (i.e., molecules with non-abelian symmetrywhere the HOMO and/or LUMO are degenerate and no unique occupation can bedefined), an error occurs and the job aborts. With such systems, you would need to runthe calculation in C1 symmetry to break the orbital degeneracy.

Static_Polarizability


off (default)

on


The Static_Polarizability keyword activates the calculation of the static molecularpolarizability tensor and first hyperpolarizability tensor, for example:

Static_Polarizability on


off:

Do not calculate static polarizability/1st hyperpolarizability.

on:

Activate static polarizability/1st hyperpolarizability calculation.

Step_Size

Options:


Turbomole E–73

Commands—Standalone Mode Swap_Alpha_Orbitals

Comm


The Step_Size keyword is used to specify the step-size taken during finite-differencenumerical frequency calculations (see Calculate keyword, page E–26), for example:

Step_Size 0.01

Where real is the value (in Bohr) of the finite-displacement step length. These numer-ical frequency calculations are carried out by displacing atomic Cartesian coordinatesby +/- real Bohr, calculating forces at each step, and constructing the force-constantmatrix (Hessian matrix) via finite-differences of the forces at the displaced geometries.

Swap_Alpha_Orbitals

Options:

pair(s) of integers


The Swap_Alpha_Orbitals keyword is used to modify the automatically generatedalpha orbital occupations for a calculation in which Spin = unrestricted. You useSwap_Alpha_Orbitals exactly like Swap_Orbitals (see page E–74); however, forSwap_Alpha_Orbitals, the pair(s) of integers are used to specify alpha (spin-up)orbital indices.

Swap_Beta_Orbitals

Options:

pair(s) of integers


The Swap_Beta_Orbitals keyword is used to modify the automatically generated betaorbital occupations for a calculation in which Spin = unrestricted. You use Swap_Beta_Orbitals exactly like Swap_Orbitals (see page E–74); however, for Swap_Beta_Orbitals, the pair(s) of integers are used to specify beta (spin-down) orbitalindices.

E–74 Turbomole

Swap_Orbitals Commands—Standalone Mode

Com

man

ds

Swap_Orbitals

Options:

pair(s) of integers


The Swap_Orbitals keyword is used to modify the automatically generated orbitaloccupations. As described above (see Spin keyword, page E–71), Turbomole automat-ically generates an aufbau orbital occupation scheme. You can modify this occupationusing the Swap_Orbitals keyword. For example, the default (aufbau) occupation forformaldehyde (C2v symmetry) is:

If you want to do your calculation on the state with 2b2 as the HOMO and 2b1 as theLUMO, you would specify:

Swap_Orbitals 8 9

in your input file.

You may include as many pairs of integers on the Swap_Orbitals line as needed todefine your non-aufbau state. In the example above, if you want to occupy orbitals 2b2and 3b1 instead of 4a1 and 5a1, you would specify Swap_Orbitals as:

Swap_Orbitals 4 9 6 11

Table E–3. Default occupation for formaldehyde

Orbital Counter Orbital Label Default Occupation

11 3b1 010 6a1 09 2b2 0

(Fermi Level)8 2b1 27 1b2 26 1b1 25 5a1 24 4a1 23 3a1 22 2a1 21 1a1 2

Turbomole E–75

Commands—Standalone Mode Symmetry

Comm

ands

Symmetry


auto (default)

string


The Symmetry keyword is used to specify how to treat the symmetry of your moleculeby selecting one of the options listed above, for example:

Symmetry d2h


auto:

Turbomole automatically determines the point-group symmetry of your mole-cule, based on the geometry provided, and uses this symmetry throughout thecalculation.

string:

The point-group symmetry is explicitly provided (with string representing thestandard symbol for the point group, e.g., c3v). For linear molecules, the twopoint group symbols to use are d*h and c*v for linear molecules with and with-out inversion centers, respectively. At present it is not possible to run a calcula-tion in a subgroup of the full symmetry of the molecule, except for C1: anymolecule can be run in C1 symmetry (i.e., without symmetry), regardless of theactual symmetry of the molecule.

If required, the Cartesian coordinates of your molecule are reoriented so that the centerof mass resides at the origin and the elements of symmetry (i.e., symmetry axes, sym-metry planes, etc.) are properly aligned with the Cartesian axis system. The exceptionto this is calculations carried out in C1 symmetry, for which molecules are not reori-ented.

E–76 Turbomole

Title Commands—Standalone Mode

Com

man

ds

Title

Options:

string


The Title keyword is used to provide a descriptive title for your job, for example:

Title DZP BLYP optimization of 3B1 methylene

Version

Options:

950300


The Version keyword is used to identify which version of the Biosym/MSI software isbeing run, for example:

Version 950

Turbomole Keywords–1

Index

AACM, E–2, E–3, E–41, E–57ACM_Coeffs, E–4, E–8ang, E–2, E–43AO_Integral_Filesize, E–3, E–9aug-cc-pvdz, E–12aug-cc-pvtz, E–12auto, E–2, E–3, E–5, E–6, E–25, E–30, E–42,

E–61, E–75

BBasis, E–2, E–10Basis_Type, E–3, E–25BFGS, E–6, E–52BFGS_safe, E–6, E–52BLYP, E–3, E–41bohr, E–2, E–43Boys_Localization, E–4, E–26BP, E–3, E–41BVWN, E–3, E–41by_element, E–2, E–10, E–14by_number, E–2, E–10, E–14B88, E–3, E–41b88, E–4, E–8, E–9

CCalculate, E–2, E–26car, E–2, E–43cartesian, E–6, E–61cc-pvdz, E–12cc-pvtz, E–12Charge, E–2, E–28coarse, E–4, E–53CONSTRAINT, E–7, E–28Constraint_Method, E–7, E–29core, E–3, E–58

DDamping, E–5, E–30default, E–5, E–38density, E–5, E–64DFT, E–2, E–57DIIS, E–6, E–31Displacement_Convergence, E–6, E–32

DMol, E–2, E–68dz, E–11dzp, E–11dzvd, E–12dzvp, E–12

EECP, E–3, E–32ECP_Range, E–3, E–33Electric_Field, E–4, E–34Electrostatic_Moments, E–4, E–35endbasis, E–10endcon, E–28end_basis, E–13, E–14end_geom, E–43, E–44, E–45energy, E–2, E–26ESP_Charges, E–5, E–36Excitation_Energy, E–5, E–36Excited_State_Method, E–5, E–37Excited_State_Multiplicity, E–5, E–38Excited_State_Symmetry, E–5, E–38

Ffile, E–2, E–10fine, E–4, E–53FIXED, E–7, E–39Frequencies, E–4, E–40frequency, E–2, E–27Freq_Dep_Polarizability, E–4, E–40Functionals, E–3, E–41

GGDIIS, E–6, E–42Geometry, E–2, E–43gradient, E–2, E–26Gradient_Convergence, E–6, E–50Grid, E–5, E–51grid1, E–51grid2, E–51grid3, E–51

HHessian_File, E–6, E–52Hessian_Update, E–6, E–52

Index of Keywords

Keywords–2 Turbomole

Index of Keywords

Inde

xHF, E–2, E–57homo, E–5, E–64huckel, E–3, E–58

IIntegration_Grid, E–4, E–53internal, E–6, E–61

KK-Pu, E–3, E–33

Llagrange, E–7, E–29lagrange/penalty, E–7, E–29Level_Shift, E–6, E–54Li-Pu, E–3, E–33local_homo, E–5, E–64local_orbital, E–5, E–64Locate, E–6, E–55Loewdin_Analysis, E–5, E–55lumo, E–5, E–64

MMax_Core_Memory, E–3, E–56Max_Displacement, E–6, E–56medium, E–4, E–53Method, E–2, E–57minimum, E–6, E–55MO_Guess, E–3, E–58MO_Integral_Filesize, E–3, E–58MP2, E–2, E–57Mulliken_Analysis, E–4, E–59Multiplicity, E–3, E–60

NNa-Pu, E–3, E–33NMR_Shielding, E–4, E–60none, E–6, E–52Number_Of_Excited_States, E–5, E–61numfreq, E–2, E–27

Ooff, E–3, E–4, E–5, E–6, E–26, E–30, E–31, E–

32, E–34, E–35, E–36, E–40, E–42, E–54, E–55, E–59, E–60, E–63, E–64, E–66, E–68, E–69, E–72

on, E–3, E–4, E–5, E–6, E–26, E–32, E–35, E–36, E–40, E–55, E–59, E–60, E–63, E–68, E–69, E–72

optimize, E–2, E–27optimize_frequency, E–2, E–27optimize_numfreq, E–2Opt_Coordinate_System, E–6, E–61Opt_Cycles, E–7, E–62Opt_Energy_Convergence, E–6, E–62Opt_Use_Symmetry, E–6, E–63orbital, E–5, E–64

Ppenalty, E–7, E–29penalty/lagrange, E–7, E–29Plot, E–5, E–64Point_Charges, E–4, E–66potential, E–5, E–64Powell, E–6, E–52Product, E–2, E–68pw, E–4, E–8, E–9

RRb-Pu, E–3, E–33Relativistic_Correction, E–4, E–68rest, E–13, E–14restricted, E–2, E–71restricted_open, E–2, E–71Roby_Davidson_Analysis, E–5, E–69rpa, E–5, E–37

SSCF_Density_Convergence, E–5, E–69SCF_Energy_Convergence, E–5, E–70SCF_Iterations, E–6, E–70sci, E–5, E–37singlet, E–5, E–38SLATER, E–3, E–41slater, E–4, E–8, E–9Spin, E–2, E–71

Turbomole Keywords–3

Index of Keywords

IndexStatic_Polarizability, E–4, E–72Step_Size, E–3, E–72sto-3g, E–11sv, E–11svp, E–11SVWN, E–3, E–41Swap_Alpha_Orbitals, E–3, E–73Swap_Beta_Orbitals, E–3, E–73Swap_Orbitals, E–3, E–74Symmetry, E–2, E–75

TTitle, E–2, E–76transition_state, E–6, E–55triplet, E–5, E–38Turbomole, E–2, E–68tz, E–11tzp, E–11tzvp, E–12tz2p, E–11

Uunc-aug-cc-pvtz, E–12unrestricted, E–2, E–71

VVersion, E–2, E–76vwn, E–4, E–8, E–9

Xxcoarse, E–4, E–53xfine, E–4, E–53xyz, E–2, E–43

ZZindo, E–2, E–68zmat, E–2, E–43, E–44

Numerics300, E–763-21g, E–115d/7f, E–3, E–25

6d/10f, E–3, E–256-31g, E–116-31g*, E–116-31g**, E–12950, E–2, E–76

Keywords–4 Turbomole

Index of Keywords

Inde

x

Turbomole Index–1

Index

AACM scheme, E–9Adams, N., A–1adiabatic connection method, E–8, E–41, E–57Ahlrichs, R., A–1, A–2, A–4all-electron methodology, E–34alpha and beta orbitals, E–71alpha orbital occupations, E–73A-matrix, E–56Amos, R. D., A–1Analyze pulldown, 4–3, 5–2Andrews, J. S., A–1Andzelm, J., 5–8, A–1, A–2Atashroo, T., A–3atomic charges, E–36atomic charges, calculating, 5–20aufbau occupation scheme, E–71aufbau orbital occupation scheme, E–74

Bbackground jobs

completion status, 5–29default host, 5–29default mode, 5–28electronic mail message, 5–29execution mode, 5–29job number, 5–28monitoring, 5–30network queuing system, 5–29, D–1notification window, 5–29requirements for running on a remote host, D–

1Background_Job pulldown, 5–1, 5–3Baker, J., 2–2, 2–3, A–1Banerjee, A., 2–4, A–1Baron, H. P., A–2Bär, M., A–1basis sets

alternative files, 5–12atom-optimized, E–11aug-cc-pvdz, 5–11aug-cc-pvtz, 5–11averaged relativistic pseudopotentials, E–15cc-pvdz, 5–11cc-pvtz, 5–11correlation-consistent, E–12custom, E–12double-zeta, 5–10

double-zeta + P, 5–10d-type, E–25dzvd, 5–10dzvp, 5–10effective core potentials, E–14f-type, E–25library, 5–9, E–10local DFT, E–12Pople-type, E–25specifying, 5–8, E–10split-valence, 5–9, E–11split-valence + P, 5–9standard choices, 5–9STO-3G, 5–10, E–11suggestions for selecting, 5–8triple-zeta, 5–10triple-zeta + P, 5–10triple-zeta + 2P, 5–10tzvp, 5–10unc-aug-cc-pvtz, 5–113-21G, 5–10, E–116-31G, 5–10, E–116-31G*, 5–10, E–116-31G**, 5–10, E–12

Becke, A. D., 5–7, A–1Becke-88 non-local exchange, E–41Becke-88 non-local exchange energy, E–8Becke-88 non-local exchange + the Lee Yang Parr

non-local correlation, E–42Becke-88 non-local exchange + the Perdew Wang

non-local correlation, E–42Becke-88 non-local exchange + the Vosko Wilk

Nusair local correlation, E–42Bergeron, D., 2–3, A–1beta orbital occupations, E–73BFGS method, E–53BiosymMSI quantum products, E–68Boggs, J. E., A–3Bone, R. G. A., A–1Boys MO localization, E–26Boys, S. F., 5–19, A–1Broyden-Fletcher-Goldfarb-Shanno Hessian up-

date method, E–53

Ccalculation

basic steps, 5–1setting up, 5–2type, E–27

Index

Index–2 Turbomole

D Index

Inde

xCartesian coordinates, E–44, E–50, E–62case-sensitivity, E–1Cerjan, C. J., 2–4, A–1Chambaud, G., A–1charge density plots, 5–20chemical shielding tensors, 5–19Christiansen, P. A., 5–12, A–2, A–3Cizek, A–1closed-shell spin state, E–71co-linear atoms, E–48commands

bold type, E–7documentation format, 1–4entering on command line in Insight program,

1–4italic type, E–7standalone, E–1

comment lines, E–1Completion_Status Background_Job, 4–3computational method, E–57constraints, E–28Constraints Optimize, 4–2, 5–24Control_Bkgd_Job Background_Job, 4–2coordinate system, E–61coordinates

Cartesian vs. internal, 2–3, 5–22specifying, 5–22switching from internal to Cartesian, 5–22

core Hamiltonian, E–58core memory, E–56Cowan-Griffin relativistic correction, E–68Cowan, R. D., 5–19, A–2CPHF equation, E–56Császár, P., 2–7, A–2Cundari, T. R., 5–12, A–2

Ddamping factor, E–30Davidson, E. R., 5–20, A–2default parameters, 5–3, C–3defining the system, 5–3density functional method, E–57density functionals, E–41density-of-states plot, 5–31Density_of_States Analyze, 4–3, 5–31DFT numerical integration grid, E–53DIIS convergence acceleration, E–31dipole moment, 5–19

direct inversion of the iterative subspace, E–31disk space, E–9, E–59Ditchfield, R., A–2doublet state, 5–15dummy atoms, 5–21, E–48Dunning, T. H., 5–11, A–2, A–3

Eeffective core potentials, 5–8, 5–9, E–14, E–32,

E–33averaged relativistic, 5–11valence basis sets, 5–11

Ehrig, M., A–2electron densities, 5–20, E–69electron density data, E–64electronic energy, computing, 5–4electronic excitations, 5–19electronic states, 5–14

closed-shell, 5–14open-shell, 5–15

electronsalpha and beta, 5–15

electrostatic charge, 5–19electrostatic moments, 5–8, E–35electrostatic potential data, E–64electrostatic potential plots, 5–20electrostatic potentials, 5–20energy grid, 5–32energy level shifting of virtual orbitals, E–54Ermler, W. C., 5–12, A–2, A–3exchange-correlation energy, E–8excitation energies, 5–8, 5–19excited-state transition energies, E–36, E–37, E–

38excited-state wavefunction, E–38executing commands in Insight environment, 5–4extended-Hückel calculation, 5–15, E–58external point charges, E–66external static electric field, E–34

Ffiles, 7–1

.arc, C–2background_job_hosts, 5–28.car, C–1, C–2, E–44, E–67control, 7–1, C–7.dos, 5–31

Turbomole Index–3

Index G

Indexformats, C–1.grd, C–2, E–64.hessian, C–2input, C–1.input, C–1, C–2, E–1.localized_mo, C–2.mdf, C–2, E–44.orig.car, C–2.outmol, 5–31, C–2, C–17output, C–2_route.csh, C–2.sum, 5–3, C–2, C–12.turbo_archive, C–7, C–2

Find_Pt_Group Symmetry, 4–2, 5–1, 5–2, 5–22finite-difference numerical frequency calcula-

tions, E–73Flannery, B. P., A–3Fletcher, R., 2–5, A–2Fogarasi, G., 2–2, A–2, A–3Foresman, J., A–2frequency-dependent molecular polarizability

tensors, E–40frequency-dependent polarizability, E–40Frisch, M., A–2

Ggeometry, E–43geometry optimization, 2–1, 5–4

algorithms, 2–3, 5–26constraint algorithms, specifying, 5–24constraints, 2–3, 5–21, E–28, E–29, E–39constraints, theory, 2–5convergence, E–32, E–50, E–63convergence criteria, 5–25DIIS convergence procedure, E–42dummy atoms, 2–3eigenvector following mode, derivation, 2–4eigenvector-following algorithm, 2–3fixed atoms, 2–3GDIIS, 2–3, 5–25, 5–26GDIIS method, theory, 2–7Hessian mode-following option, 2–3maximum cycles, E–62minimum, E–55procedure, 5–21starting geometry, 2–3strategy, 2–1transition state, E–55

geometry update vector, E–56Get Contour, 5–32Godbout, N., 5–10, A–2

gradients, 5–4grid

resolution, 5–27setting up, 5–27

Griffin, D. C., 5–19, A–2

HHaase, F., A–2Handy, N. C., A–1Harrison, R. J., A–3Hartree-Fock exchange energy, E–8Hartree-Fock method, E–57Häser, M., A–1, A–2, A–4Head–Gordon, M., A–2heavy elements, 5–2Hehre, W. J., 2–3, 5–10, A–1, A–3help, on-line, 1–4Hessian matrix, 5–21, E–52

advantages, 5–22generating, 5–26specifying, 5–24starting, 5–22update method, 5–26updating, E–52

highest occupied molecular orbital plots, 5–20highest occupied molecular orbital (HOMO) data,

E–64Horn, H., A–1, A–2, A–4host

local, D–1preferred, 5–28remote, D–1

Hout, R. F. Jr., 5–30Hurley, M. M., 5–12, A–3hybrid DFT/Hartree-Fock method, E–57hyperpolarizability tensor, E–72

Iinfrared absorption intensities, 5–4, 5–8internal coordinates, E–50, E–62irreducible representation, E–39

JJayatilaka, D., A–1

Index–4 Turbomole

K Index

Inde

x

KKendall, R. A., 5–11, A–3keywords, 7–1

additional job control, 7–2control of geometry optimization, 7–5controlling calculation of properties, 7–3controlling the external environment, 7–3DFT-specific, 7–3header, 7–1primary job control, 7–1SCF tolerances and convergence control, 7–5values, types of, E–7

Kill_Bkgd_Job Background_Job, 4–3Kobayashi, H., A–3Koga, T., A–3Kölmel, C., A–1

LLagrange multiplier algorithm, 5–24Lagrange multipliers, E–29LaJohn, L. A., 5–12, A–3Levy, B., A–1linear mixing coefficients, E–8Loewdin population analysis, 5–20, E–55lowest unoccupied molecular orbital plots, 5–20lowest unoccupied molecular orbital (LUMO) da-

ta, E–65

Mmagnetic shielding tensor, E–60Miller, W. H., 2–4, A–1Millie, P., A–1minima, locating, 2–1molecular

electrostatic moments, 5–19electrostatic polarizability, 5–20interactions, weak, 5–8orbitals, plotting, 5–20

molecular charge, 5–14molecular energy at fixed geometry, E–27molecular energy + atomic forces at fixed geome-

try, E–27molecular geometry optimization, E–27molecular orbitals, 5–20molecular polarizability tensor, E–72Moller-Plesset perturbation theory, E–57MOs from a file, E–58

MOs from previous calculation, reusing, 5–18MP2 energy, 5–9Mulliken population analysis, 5–20, E–56, E–59Mulliken, R. S., 5–20, A–3

NNesbet, R. K., A–3NMR shieldings, 5–9non-abelian symmetry, E–72normal modes, 5–31Normal_Mode Analyze, 4–3, 5–31N-phenylbenzamide, E–13number of excited states, E–61

Oopen-shell spin state, E–71open-shell system, specifying spin, 5–15Optimize pulldown, 4–2, 5–1, 5–2Opt_Parameters Optimize, 4–2orbital degeneracy, E–72orbital occupations, 5–14orbitals

contouring, 5–30degeneracy, 5–15degenerate, 5–20SCF, 5–15triply degenerate, 5–21virtual, 5–9

Orbital_Contour Analyze, 4–3, 5–30oscillator strengths, 5–19, E–37, E–38

PPacios, L. F., 5–12, A–3Paldus, A–1Pang, F., A–3Parameters Setup, 4–1, 5–1penalty functions, E–29plotting, E–51, E–64

multiple options, E–65point charges, E–66point-group symmetry, 5–2polarizabilities, 5–8polarization functions, 5–8Pople, J. A., A–2, A–3population analysis, 5–20Powell Hessian update method, E–53

Turbomole Index–5

Index R

IndexPowers, J. M., A–3preparing the molecule, 5–2Press, W. H., A–3Pseudo_Atom pulldown, 5–21Pulay, P., 2–3, 2–7, 5–25, A–2, A–3PW-91 non-local correlation energy, E–8

RRadom, L., A–3random phase approximation method, E–37results

examining, 5–3reliability, 5–8

rings, E–49Roby–Davidson population analysis, E–69Roby, K. R., 5–20, A–3Roothaan, C. C. J., A–3Ross, R. B., 5–12, A–2, A–3run conditions, 5–3Run pulldown, 4–3, 5–1running the Turbomole job, 5–3run-time directory, 8–1Run_Turbomole Run, 4–3, 5–3, 5–29

SSalahub, D. R., A–2Scan_DMol_Output Analyze, 5–31Scan_TMol_Output Analyze, 4–3SCF

canonical molecular orbitals, 5–19convergence, E–54, E–69, E–70convergence criteria, 5–18direct and indirect methods, 5–13disk space, 5–13energy, relativistic correction, 5–19maximum iterations, E–70setting up calculation, 5–15smooth convergence, E–30

Schäfer, A., 5–9, 5–10, A–4Scheiner, A., A–1Schlegel, H. B., A–4Schleyer, P. v. R., A–3Setup pulldown, 4–1, 5–2Setup_Bkgd_Job Background_Job, 4–2Setup_Grid_Output Setup, 4–2, 5–1, 5–27shallow minima, 5–26Shepard, R., A–1Simons, J., A–1

singles CI method, E–37singlet excited states, E–38singlet state, 5–15Slater local exchange, E–42Slater local exchange energy, E–8Slater local exchange + the Vosko Wilk Nusair lo-

cal correlation, E–42spatial symmetry, E–38specific MOs, E–65spin multiplicity, 5–15, E–38, E–60spin states, 5–14, 5–15standalone mode, running Turbomole, 8–1starting SCF orbitals, E–58starting Turbomole, 5–1, 5–3

in standalone mode, 1–3in the Insight environment, 1–3

stationary point, E–55Stevens, W. J., 5–12, A–2symmetry, 5–4, 5–22, 5–25, E–63, E–75System Setup, 4–1, 5–1, 5–2, 5–3system size, 5–2

TTaylor, P. W., A–2title, E–76total molecular charge, E–28transition oscillator strengths, E–36transition states, 5–25, 5–26

locating, 2–1triplet excited states, E–38triplet state, 5–15Tuekolsky, S. A., A–3Turbomole

Insight and standalone modes, 1–2two-electron integrals, E–9, E–59

form, 5–13type of calculation, choosing, 5–4

Uunits, E–44UV/visible spectrum, 5–19

Vversion, E–76Vetterling, W. T., A–3vibrational

Index–6 Turbomole

W Index

Inde

xfrequencies, 5–25frequencies and intensities, 5–4

vibrational frequencies + IR intensities, E–27virtual orbitals, E–54VWN local correlation energy, E–8

Wwavefunctions

SCF, 5–15spin-restricted, 5–15spin-unrestricted, 5–15

Weiss, H., A–4Weis, P., A–2Wimmer, E., A–2Wrinn, M., A–1

ZZhou, X., A–2Z-matrix, 2–2z-matrix, E–44

Numerics3D data generation, 5–27

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