Interface turbomole

Interface to the Turbomole computational chemistry package (www.turbomole-gmbh.com, commercial software). Turbomole provides very fast implementation of DFT and wavefunction methods.

Warning

Construction of the inputs for turbomole is difficult and problems may appear when moving to different version of turbomole. Moreover, some problems may get unnoticed as the calculation can run successfully, ignoring some part of the input. It is recommended to check the turbomole outputs manually for each type of calculation before production calculations.

News

Jan 2019: Several keywords for configuring turbomole (turbomole_bin_dir_*) were removed, as they were not used for some time. If you have these in your config file, Cuby will complain about it – it is safe to remove them.

Memory specification

Turbomole does use a limit on memory that is allocated. Rather than that, the size of a core memory allocated in advance for some data is specified, and the remaining memory is allocated dynamically. To make this scheme compatible with cuby, the mem keyword is used to specify the size of the memory available on the node, and keyword mem_core specifies the percentage of core memory reserved. Keywords mem_core_scf and mem_core_correlation provide a finer control, overriding the value of mem_core if set.

In versions prior 7.3, specifying the size of core memory for parallel calculations was a mess (it was not clear in which case memory per node or per core should be specified). Generally, cuby uses memory per node, and attempts to convert it to the value turbomole expects, but this may not be correct for each version of turbomole. In Turbomole 7.3, all memory can be defined as per node what removes any ambiguity, and cuby uses this option.

COSMO-RS calculations

Cuby interfaces also the COSMO-RS software that provides advanced method for calculation of solvation free energies on the basis of COSMO calculations in turbomole. For now, the interface supports only BP/def2-TZVPD level of calculation and a single solvent, water. An example is provided below (Example 5).

Methods and capabilities

The interface implements following methods (specified by keyword 'method'):

hf - supports calculation of energy, gradient, hessian, atomic_charges, point_charges, point_charges_gradient, mos
mp2 - supports calculation of energy, gradient
mp3 - supports calculation of energy
dft - supports calculation of energy, gradient, hessian, atomic_charges, point_charges, point_charges_gradient, mos
ccsd - supports calculation of energy
ccsd(t) - supports calculation of energy, point_charges
rpa - supports calculation of energy
am1 - supports calculation of energy, atomic_charges

The interface implements following solvent models (keyword 'solvent_model'):

cosmo
cosmo_rs

The interface implements following atomic charge types (keyword 'atomic_charges'):

nbo - Natural bond orbital (NBO) charges
mulliken - Mulliken charges
esp - ESP charges

Keywords used

Keywords specific for this interface:

Other keywords used by this interface:

Examples

The following examples, along with all other files needed to run them, can be found in the directory cuby4/interfaces/turbomole/examples

#===============================================================================
# Turbomole example 1 - configuration
#===============================================================================

# Example of a full configuration of the interface. The following examples
# assume that this configuration is done in the configuration file.

# Configuration of the interface (change the paths to your installation)
# Version of Turbomole
turbomole_version: 6.6
# The base diretory of the Turbomole installation
turbomole_turbodir: /home/rezac/bin/turbomole/turbomole-6.6/arch/all
# Path to serial binaries
turbomole_bin_dir: /home/rezac/bin/turbomole/turbomole-6.6/arch/all/bin/em64t-unknown-linux-gnu
# Path to all flavours of parallel binaries
turbomole_bin_dir_smp: /home/rezac/bin/turbomole/turbomole-6.6/arch/all/bin/em64t-unknown-linux-gnu_smp
turbomole_bin_dir_mpi: /home/rezac/bin/turbomole/turbomole-6.6/arch/all/bin/em64t-unknown-linux-gnu_mpi
turbomole_bin_dir_mpi: /home/rezac/bin/turbomole/turbomole-6.6/arch/all/bin/em64t-unknown-linux-gnu_ga
# Path to Turbomole scripts
turbomole_scripts_dir: /home/rezac/bin/turbomole/turbomole-6.6/arch/all/scripts

# Simple calculation: water dimer at HF/def2-SVP level
job: energy
interface: turbomole
geometry: A24:water
charge: 0
basisset: def2-SVP
method: hf

#===============================================================================
# Turbomole example 2 - Methods
#===============================================================================

# This example run a calculation of water molecule with all  methods available
# in this interface

job: multistep
steps: hf, rihf, rimp2, rimp2rihf, rimp3, ccsd, ccsdt, dft

# Common setup for all steps
calculation_common:
  job: energy
  interface: turbomole
  geometry: A24:water
  charge: 0
  basisset: def2-SVP

# HF
calculation_hf:
  method: hf
  density_fitting: none # Disable the RI approximation

# RI-HF
calculation_rihf:
  method: hf
  # RI is on by default

# RI-MP2, full HF
calculation_rimp2:
  method: mp2
  density_fitting: correlation

# RI-MP2 on RI-HF
calculation_rimp2rihf:
  method: mp2
  density_fitting: both # (this is the default)

# RI-MP3
calculation_rimp3:
  method: mp3

# CCSD
calculation_ccsd:
  method: ccsd

# CCSD(T)
calculation_ccsdt:
  method: ccsd(t)

# DFT
calculation_dft:
  method: dft
  functional: b3-lyp

#===============================================================================
# Turbomole example 3 - mixing basis sets
#===============================================================================

# Calculation with custom basis set and auxiliary basis sets. This particular
# setup makes no sense but demonstrates all the options.

# Calculation setup
job: energy
interface: turbomole
geometry: A24:water
charge: 0
method: mp2
density_fitting: both # RI for both HF and MP2 steps

# Default AO basis:
basisset: def2-SVP

# Auxiliary basis for RI-HF
auxiliary_basis_scf: def2-TZVP

# Auxiliary basis for RI-MP2
auxiliary_basis_mp2: aug-cc-pVDZ

# Change basis sets for some elements
basisset_elements:
  H: def2-TZVP
auxiliary_basis_scf_elements: 
  O: aug-cc-pVDZ
auxiliary_basis_mp2_elements:
  H: aug-cc-pVTZ

#===============================================================================
# Turbomole example 4 - COSMO solvation
#===============================================================================

# Calculation of a solvation energy using the COSMO model

job: energy
# Mixer interface is used to get the difference between COSMO and gas-phase energies
interface: mixer

mixer_weight_a: 1.0
mixer_weight_b: -1.0

geometry: A24:water

calculation_common:
  interface: turbomole
  charge: 0
  basisset: def2-SVP
  method: dft
  functional: b-lyp

calculation_a: # Gas phase
  charge: 0 # Could be empty, but something bust be here

calculation_b: # COSMO water
  solvent_model: cosmo
  solvent_epsilon: 78.5

#===============================================================================
# Turbomole example 5 - COSMO-RS solvation
#===============================================================================

# Calculation of a solvation energy using the COSMO-RS model
# (requires additional software, COSMOtherm)

# It is assumed that the path to COSMOtherm (keyword turbomole_cosmotherm_dir)
# is set up in a configuration file

# The solvation free energy is printed as energy in the output

job: energy
interface: turbomole

solvent_model: cosmo_rs
# For now, the interface supports only the following solvent:
solvent_name: h2o

# The interface supports only the following calculation setup for which
# COSMO-RS was parametrized
method: dft
functional: B-P
basisset: def2-TZVPD

geometry: A24:methane
charge: 0