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