Jobs¶

Basic Jobs¶

All Jobs prepended with Scine indicate that they are making use of the C++ module interface defined in SCINE. Hence, adding a personal module with a custom Calculator will automatically enable the use of these tasks with the custom module/Calculator.

For more information about this interface please see the documentation of SCINE: Core and possibly also SCINE: Utils.

Conformer Generation¶

class scine_puffin.jobs.conformers.Conformers[source]¶

A job generating all possible conformers (guesses) for a given structure with molassembler. The given model is used as a hint for the quality of the bond orders that are to be used when generating the molassembler molecule.

Order Name

conformers

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

add_based_on_distance_connectivity :: bool: If True, the structure’s connectivity is derived from interatomic distances via the utils.BondDetector: The bond orders used for interpretation are set to the maximum between those given in the bond_orders property and 1.0, whereever the utils.BondDetector detects a bond. (default: True)
sub_based_on_distance_connectivity :: bool: If True, the structure’s connectivity is derived from interatomic distances via the utils.BondDetector: The bond orders used for interpretation are removed, whereever the utils.BondDetector does not detect a bond. (default: True)
enforce_bond_order_model :: bool: If True, only processes bond_orders that were generated with the specified model. If False, eventually falls back to any bond_orders available for the structure. (default: True)
dihedral_retries :: int: The number of attempts to generate the dihedral decision during conformer generation. (default: 100)

Required Packages

SCINE: Database (present by default)
SCINE: molassembler (present by default)
SCINE: Utils (present by default)

Generated Data

If successful the following data will be generated and added to the database:

Structures: A set of conformers guesses derived from the graph representation of the initial structure. All generated conformers will have a graph (masm_cbor_graph) and decision list set (masm_decision_list).

SCINE: AFIR¶

class scine_puffin.jobs.scine_afir.ScineAfir[source]¶

A job optimizing a structure while applying an artificial force.

Order Name

scine_afir

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are: All settings recognized by ReaDuct’s AFIR task. For a complete list see the ReaDuct manual The most common AFIR related ones being:

afir_afir_weak_forces :: bool: This activates an additional, weakly attractiveforce applied to all atom pairs. By default set to False.
afir_afir_attractive :: bool: Specifies whether the artificial force is attractive or repulsive. By default set to True, which means that the force is attractive.
afir_afir_rhs_list :: List[int]: This specifies list of indices of atoms to be artificially forced onto or away from those in the LHS list (see below). By default, this list is empty. Note that the first atom has the index zero.
afir_afir_lhs_list :: List[int]: This specifies list of indices of atoms to be artificially forced onto or away from those in the RHS list (see above). By default, this list is empty. Note that the first atom has the index zero.
afir_afir_energy_allowance :: float: The maximum amount of energy to be added by the artificial force, in kJ/mol. By default set to 1000 kJ/mol.
afir_afir_phase_in :: int: The number of steps over which the full force is gradually applied. By default set to 100.

All settings that are recognized by the SCF program chosen.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful the following data will be generated and added to the database:

Structures: A new structure, the optimized (inc. artificial force) structure.
Properties: The electronic_energy associated with the new structure.

SCINE: Bond Orders¶

class scine_puffin.jobs.scine_bond_orders.ScineBondOrders[source]¶

A job calculating bond orders.

Order Name

scine_bond_orders

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

only_distance_connectivity :: bool: Whether the bond orders shall be constructed via distance information only (True) or from an electronic structure calculation (False). (default: False)
add_based_on_distance_connectivity :: bool: If True, the structure’s connectivity is derived from interatomic distances via the utils.BondDetector: The bond orders used for interpretation are set to the maximum between those given by an electronic structure calculation and 1.0, whereever the utils.BondDetector detects a bond. (default: True)
sub_based_on_distance_connectivity :: bool: If True, the structure’s connectivity is derived from interatomic distances via the utils.BondDetector: The bond orders used given by an electronic structure calculation are removed, whereever the utils.BondDetector does not detect a bond. (default: True)
add_graph :: bool: Whether to add a molassembler graph and decision list to the structure based on the determined bond orders. (default: True)

All settings that are recognized by the SCF program chosen.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: molassembler (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful the following data will be generated and added to the database:

Properties: The bond_orders (SparseMatrixProperty) are added. Optionally the electronic_energy associated with the structure if it is present in the results of provided by the calculator interface.
Other: If a graph is requested, graph representations of the structure will be added to the structures graphs field. The added representations are: A representation of the graph masm_cbor_graph, and the decision representations of the existing stereopermutators using a nearest neighbour fit masm_decision_list. Any previous graph representations of the structure will be overwritten.

SCINE: Geometry Optimization¶

class scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization[source]¶

A job optimizing the geometry of a given structure, in search of a local minimum on the potential energy surface. Optimizing a given structure’s geometry, generating a new minimum energy structure, if successful.

Order Name

scine_geometry_optimization

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

All settings recognized by ReaDuct’s geometry optimization task.

Common examples are:

optimizer :: str: The name of the optimizer to be used, e.g. ‘bfgs’, ‘lbfgs’, ‘nr’ or ‘sd’.
convergence_max_iterations :: int: The maximum number of geometry optimization cycles.
convergence_delta_value :: float: The convergence criterion for the electronic energy difference between two steps.
convergence_gradient_max_coefficient :: float: The convergence criterion for the maximum absolute gradient. contribution.
convergence_step_rms :: float: The convergence criterion for root mean square of the geometric gradient.
convergence_step_max_coefficient :: float: The convergence criterion for the maximum absolute coefficient in the last step taken in the geometry optimization.
convergence_gradient_rms :: float: The convergence criterion for root mean square of the last step taken in the geometry optimization.

For a complete list see the ReaDuct manual

All settings that are recognized by the SCF program chosen.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful the following data will be generated and added to the database:

Structures: A new minimum energy structure.
Properties: The electronic_energy associated with the new structure.

SCINE: Hessian¶

class scine_puffin.jobs.scine_hessian.ScineHessian[source]¶

A job generating a Hessian and derived data for a single structure. Derived data means the eigenvalues (frequencies) and eigenvectors (normalmodes) as well as thermochemical data (Gibbs free energy).

Order Name

scine_hessian

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

All settings recognized by ReaDuct’s Hessian task. For a complete list see the ReaDuct manual

All settings that are recognized by the SCF program chosen.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful the following data will be generated and added to the database:

Properties: The hessian (DenseMatrixProperty), frequencies (VectorProperty), normal_modes (DenseMatrixProperty), gibbs_energy_correction (NumberProperty) and gibbs_free_energy` (``NumberProperty) will be provided. Optionally the electronic_energy associated with the structure if it is present in the results of provided by the calculator interface.

SCINE: IRC Scan¶

class scine_puffin.jobs.scine_irc_scan.ScineIrcScan[source]¶

A job scanning a single intrinsic reaction coordinate.

Order Name

scine_irc_scan

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

All settings recognized by ReaDuct’s IRC task. For a complete list see the ReaDuct manual

Common examples are:

stop_on_error :: bool: If False, the optimization does not need to fully converge but will be accepted as a success even if it reaches the maximum amounts of optimization cycles. Also the resulting structures will be flagged as minimum_guess if this option is set ot be False. (Default: True)
irc_mode :: int: The mode to follow during the IRC scan. By default the first mode (0). (mode with the larges imaginary frequency will be followed).

All settings that are recognized by the SCF program chosen.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful the following data will be generated and added to the database:

Structures: Both the forward and backward optimized structures will be added to the database. They will be flagged as: minimum_optimized or minimum_guess if stop_on_error is set to False.
Properties: The electronic_energy associated with both forward and backward structures.

SCINE: Artificial Force Induced Reaction Probe¶

class scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir[source]¶

A job that tries to enforce a reaction, given a reactive complex and its parts. The reactive complex is expected to be generated as two structures placed next to one another or, for intramolecular reactions, to be equal to the start structure. The job then forces the specified sites of the structure(s) onto one another and analyzes the resulting structure(s) when relaxing. Alternatively, pushing apart the specified sites can be evoked via the AFIR settings.

The list of calculations/steps done is the following:

Set up of a reactive complex based on the given specifications

Enforce collision of structure (AFIR optimization)

Relaxation of the AFIR result (free optimization)

Check if new structures were formed. If not, stop.

Optimization of a minimum energy pathway connecting start and end, generation of a transition state (TS) guess.

Optimization of the TS guess to the actual TS.

Hessian calculation of the TS structure

Validate the TS using a combination of IRC scan and optimization of the resulting structures.

Check if the IRC matches start and endpoint. If not, stop.

Optimize the products separately.

Store the new elementary step in the database.

Order Name

scine_react_complex_afir

Required Input

The reactive complex, and the structures it was made from in the list of structures handed to the task. If only one structure is provided, an intramolecular reaction is set up. Furthermore, the reactive sites in the complex that shall be pressed onto one another need to be given using:

afir_afir_rhs_list :: int: This specifies list of indices of atoms to be artificially forced onto or away from those in the LHS list.
afir_afir_lhs_list :: int: This specifies list of indices of atoms to be artificially forced onto or away from those in the RHS list.

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. All possible settings for this job are based on those available in SCINE Readuct. For a complete list see the ReaDuct manual

Given that this job does more than one, in fact many separate calculations it is possible to target each individually with the settings. In order to achieve this each regular setting, such as convergence_max_iterations has to be prepended with a tag, identifying which part of the job it is meant to impact. If the setting is meant to be added to the IRC scan at the end of this job irc_convergence_max_iterations should be used. Note that this may include a doubling of this style of flags, as Readuct uses a similar way of sorting options. Hence, choosing a none default irc_mode in this task has to be done using irc_irc_mode.

The complete list prefixes for specific settings for the steps listed at the start of this section is:

AFIR optimization: afir_*

Relaxation of the AFIR result (free optimization): opt_*

Optimization of a minimum energy pathway: bspline_*

TS optimization: tsopt_*

Validation using an IRC scan: irc_*

Optimization of the structures obtained with the IRC scan : ircopt_*

Optimization of new products: opt_*

The following options are available for the reactive complex generation:

rc_x_alignment_0 :: List[float], length=9: In case of two structures building the reactive complex, this option describes a rotation of the first structure (index 0) that aligns the reaction coordinate along the x-axis (pointing towards +x). The rotation assumes that the geometric mean position of all atoms in the reactive site (afir_lhs_list) is shifted into the origin.
rc_x_alignment_1 :: List[float], length=9: In case of two structures building the reactive complex, this option describes a rotation of the second structure (index 1) that aligns the reaction coordinate along the x-axis (pointing towards -x). The rotation assumes that the geometric mean position of all atoms in the reactive site (afir_rhs_list) is shifted into the origin.
rc_x_rotation :: float: In case of two structures building the reactive complex, this option describes a rotation angle around the x-axis of one of the two structures after rc_x_alignment_0 and rc_x_alignment_1 have been applied.
rc_x_spread :: float: In case of two structures building the reactive complex, this option gives the distance by which the two structures are moved apart along the x-axis after rc_x_alignment_0, rc_x_alignment_1, and rc_x_rotation have been applied.
rc_displacement :: float: In case of two structures building the reactive complex, this option adds a random displacement to all atoms (random direction, random length). The maximum length of this displacement (per atom) is set to be the value of this option.
rc_spin_multiplicity :: int: This option sets the spin_multiplicity of the reactive complex. In case this is not given the spin_multiplicity of the initial structure or minimal possible spin of the two initial structures is used.
rc_molecular_charge :: int: This option sets the molecular_charge of the reactive complex. In case this is not given the molecular_charge of the initial structure or sum of the charges of the initial structures is used. Note: If you set the rc_molecular_charge to a value different from the sum of the start structures charges the possibly resulting elementary steps will never be balanced but include removal or addition of electrons.
rc_minimal_spin_multiplicity :: bool: True: The total spin multiplicity in a bimolecular reaction is based on the assumption of total spin recombination (s + t = s; t + t = s; d + s = d; d + t = d) False: No spin recombination is assumed (s + t = t; t + t = quin; d + s = d; d + t = quar) (default: False)

The following settings are recognized without a prepending flag:

add_based_on_distance_connectivity :: bool: Whether to add the connectivity (i.e. add bonds) as derived from atomic distances when graphs are generated. (default: True)
sub_based_on_distance_connectivity :: bool: Whether to subtract the connectivity (i.e. remove bonds) as derived from atomic distances when graphs are generated. (default: True)
only_distance_connectivity :: bool: Whether to impose the connectivity solely from distances. (default: False)
imaginary_wavenumber_threshold :: float: Threshold value in inverse centimeters below which a wavenumber is considered as imaginary when the transition state is analyzed. Negative numbers are interpreted as imaginary. (default: 0.0)
spin_propensity_check :: int: The range to check for possible multiplicities for products. A value of 2 (default) will check triplet and quintet for a singlet and will check singlet, quintet und septet for triplet.

Additionally all settings that are recognized by the SCF program chosen. are also available. These settings are not required to be prepended with any flag.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: molassembler (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful (technically and chemically) the following data will be generated and added to the database:

Elementary Steps: If found, a single new elementary step with the associated transition state will be added to the database.
Structures: The transition state (TS) and also the separated products will be added to the database.
Properties: The hessian (DenseMatrixProperty), frequencies (VectorProperty), normal_modes (DenseMatrixProperty), gibbs_energy_correction (NumberProperty) and gibbs_free_energy (NumberProperty) of the TS will be provided. The electronic_energy associated with the TS structure and each of the products will be added to the database.

SCINE: Newton Trajectory Reaction Probe¶

class scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt[source]¶

A job that tries to force a reaction, given a reactive complex and its parts. The reactive complex is expected to be generated as two structures placed next to one another. The job then forces groups of atoms onto or away from one another and analyzes the resulting structure(s) when relaxing. Only one pair of atom groups is allowed, and only repulsion or attraction of said groups can be screened at a time.

The list of calculations/steps done is the following:

Set up of a reactive complex based on the given specifications

Enforce collision of structure (NT optimization), and extraction of a transition state (TS) guess

Optimization of the TS guess to the actual TS.

Hessian calculation of the TS structure

Validate the TS using a combination of IRC scan and optimization of the resulting structures.

Check if the IRC generated the input on one side and a new set of structures on the other side of the TS.

Optimize the products separately.

Store the new elementary step in the database.

Order Name

scine_react_complex_nt

Required Input

The reactive complex (the structures it is made from) has to be defined in the list of structures handed to the task. If only one structure is provided, an intramolecular reaction is set up. Furthermore, the reactive sites in the complex that shall be pressed onto one another need to be given using:

nt_nt_rhs_list :: int: This specifies list of indices of atoms to be forced onto or away from those in the LHS list.
nt_nt_lhs_list :: int: This specifies list of indices of atoms to be forced onto or away from those in the RHS list.

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. All possible settings for this job are based on those available in SCINE Readuct. For a complete list see the ReaDuct manual

Given that this job does more than one, in fact many separate calculations it is possible to target each individually with the settings. In order to achieve this each regular setting, such as convergence_max_iterations has to be prepended with a tag, identifying which part of the job it is meant to impact. If the setting is meant to be added to the IRC scan at the end of this job irc_convergence_max_iterations should be used. Note that this may include a doubling of this style of flags, as Readuct uses a similar way of sorting options. Hence, choosing a none default irc_mode in this task has to be done using irc_irc_mode.

The complete list prefixes for specific settings for the steps listed at the start of this section is:

Reactive complex generation rc_*

Newton trajectory scan: nt_*

TS optimization: tsopt_*

Validation using an IRC scan: irc_*

Optimization of the structures obtained with the IRC scan : ircopt_*

Optimization of new products: opt_*

The following options are available for the reactive complex generation:

rc_x_alignment_0 :: List[float], length=9: In case of two structures building the reactive complex, this option describes a rotation of the first structure (index 0) that aligns the reaction coordinate along the x-axis (pointing towards +x). The rotation assumes that the geometric mean position of all atoms in the reactive site (nt_lhs_list) is shifted into the origin.
rc_x_alignment_1 :: List[float], length=9: In case of two structures building the reactive complex, this option describes a rotation of the second structure (index 1) that aligns the reaction coordinate along the x-axis (pointing towards -x). The rotation assumes that the geometric mean position of all atoms in the reactive site (nt_rhs_list) is shifted into the origin.
rc_x_rotation :: float: In case of two structures building the reactive complex, this option describes a rotation angle around the x-axis of one of the two structures after rc_x_alignment_0 and rc_x_alignment_1 have been applied.
rc_x_spread :: float: In case of two structures building the reactive complex, this option gives the distance by which the two structures are moved apart along the x-axis after rc_x_alignment_0, rc_x_alignment_1, and rc_x_rotation have been applied.
rc_displacement :: float: In case of two structures building the reactive complex, this option adds a random displacement to all atoms (random direction, random length). The maximum length of this displacement (per atom) is set to be the value of this option.
rc_spin_multiplicity :: int: This option sets the spin_multiplicity of the reactive complex. In case this is not given the spin_multiplicity of the initial structure or minimal possible spin of the two initial structures is used.
rc_molecular_charge :: int: This option sets the molecular_charge of the reactive complex. In case this is not given the molecular_charge of the initial structure or sum of the charges of the initial structures is used. Note: If you set the rc_molecular_charge to a value different from the sum of the start structures charges the possibly resulting elementary steps will never be balanced but include removal or addition of electrons.
rc_minimal_spin_multiplicity :: bool: True: The total spin multiplicity in a bimolecular reaction is based on the assumption of total spin recombination (s + t = s; t + t = s; d + s = d; d + t = d) False: No spin recombination is assumed (s + t = t; t + t = quin; d + s = d; d + t = quar) (default: False)

The following settings are recognized without a prepending flag:

add_based_on_distance_connectivity :: bool: Whether to add the connectivity (i.e. add bonds) as derived from atomic distances when graphs are generated. (default: True)
sub_based_on_distance_connectivity :: bool: Whether to subtract the connectivity (i.e. remove bonds) as derived from atomic distances when graphs are generated. (default: True)
only_distance_connectivity :: bool: Whether to impose the connectivity solely from distances. (default: False)
imaginary_wavenumber_threshold :: float: Threshold value in inverse centimeters below which a wavenumber is considered as imaginary when the transition state is analyzed. Negative numbers are interpreted as imaginary. (default: 0.0)
spin_propensity_check :: int: The range to check for possible multiplicities for products. A value of 2 (default) will check triplet and quintet for a singlet and will check singlet, quintet und septet for triplet.

Additionally all settings that are recognized by the SCF program chosen. are also available. These settings are not required to be prepended with any flag.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: molassembler (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful (technically and chemically) the following data will be generated and added to the database:

Elementary Steps: If found, a single new elementary step with the associated transition state will be added to the database.
Structures: The transition state (TS) and also the separated products will be added to the database.
Properties: The hessian (DenseMatrixProperty), frequencies (VectorProperty), normal_modes (DenseMatrixProperty), gibbs_energy_correction (NumberProperty) and gibbs_free_energy (NumberProperty) of the TS will be provided. The electronic_energy associated with the TS structure and each of the products will be added to the database.

SCINE: Newton Trajectory 2 Reaction Probe¶

class scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2[source]¶

A job that tries to force a reaction, given a reactive complex and its parts. The reactive complex is expected to be generated as two structures placed next to one another. The job then forces pairs of atoms onto or away from one another and analyzes the resulting structure(s) when relaxing. Multiple pairs and mixed choices for their movements are allowed in this version of the Newton Trajectory job.

The list of calculations/steps done is the following:

Set up of a reactive complex based on the given specifications

Enforce collision of structure (NT2 optimization), and extraction of a transition state (TS) guess

Optimization of the TS guess to the actual TS.

Hessian calculation of the TS structure

Validate the TS using a combination of IRC scan and optimization of the resulting structures.

Check if the IRC generated the input on one side and a new set of structures on the other side of the TS.

Optimize the products separately.

Store the new elementary step in the database.

Order Name

scine_react_complex_nt2

Required Input

The reactive complex (the structures it is made from) has to be defined in the list of structures handed to the task. If only one structure is provided, an intramolecular reaction is set up. Furthermore, the reactive sites in the complex that shall be pressed onto one another need to be given using:

nt_nt_associations :: int: This specifies list of indices of atoms pairs to be forced onto another. Pairs are given in a flat list such that indices 2i and 2i+1 form a pair.
nt_nt_dissociations :: int: This specifies list of indices of atoms pairs to be forced away from another. Pairs are given in a flat list such that indices 2i and 2i+1 form a pair.

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. All possible settings for this job are based on those available in SCINE Readuct. For a complete list see the ReaDuct manual

Given that this job does more than one, in fact many separate calculations it is possible to target each individually with the settings. In order to achieve this each regular setting, such as convergence_max_iterations has to be prepended with a tag, identifying which part of the job it is meant to impact. If the setting is meant to be added to the IRC scan at the end of this job irc_convergence_max_iterations should be used. Note that this may include a doubling of this style of flags, as Readuct uses a similar way of sorting options. Hence, choosing a none default irc_mode in this task has to be done using irc_irc_mode.

The complete list prefixes for specific settings for the steps listed at the start of this section is:

Reactive complex generation rc_*

Newton trajectory scan: nt_*

TS optimization: tsopt_*

Validation using an IRC scan: irc_*

Optimization of the structures obtained with the IRC scan : ircopt_*

Optimization of new products: opt_*

The following options are available for the reactive complex generation:

rc_x_alignment_0 :: List[float], length=9: In case of two structures building the reactive complex, this option describes a rotation of the first structure (index 0) that aligns the reaction coordinate along the x-axis (pointing towards +x). The rotation assumes that the geometric mean position of all atoms in the reactive site (nt_lhs_list) is shifted into the origin.
rc_x_alignment_1 :: List[float], length=9: In case of two structures building the reactive complex, this option describes a rotation of the second structure (index 1) that aligns the reaction coordinate along the x-axis (pointing towards -x). The rotation assumes that the geometric mean position of all atoms in the reactive site (nt_rhs_list) is shifted into the origin.
rc_x_rotation :: float: In case of two structures building the reactive complex, this option describes a rotation angle around the x-axis of one of the two structures after rc_x_alignment_0 and rc_x_alignment_1 have been applied.
rc_x_spread :: float: In case of two structures building the reactive complex, this option gives the distance by which the two structures are moved apart along the x-axis after rc_x_alignment_0, rc_x_alignment_1, and rc_x_rotation have been applied.
rc_displacement :: float: In case of two structures building the reactive complex, this option adds a random displacement to all atoms (random direction, random length). The maximum length of this displacement (per atom) is set to be the value of this option.
rc_spin_multiplicity :: int: This option sets the spin_multiplicity of the reactive complex. In case this is not given the spin_multiplicity of the initial structure or minimal possible spin of the two initial structures is used.
rc_molecular_charge :: int: This option sets the molecular_charge of the reactive complex. In case this is not given the molecular_charge of the initial structure or sum of the charges of the initial structures is used. Note: If you set the rc_molecular_charge to a value different from the sum of the start structures charges the possibly resulting elementary steps will never be balanced but include removal or addition of electrons.
rc_minimal_spin_multiplicity :: bool: True: The total spin multiplicity in a bimolecular reaction is based on the assumption of total spin recombination (s + t = s; t + t = s; d + s = d; d + t = d) False: No spin recombination is assumed (s + t = t; t + t = quin; d + s = d; d + t = quar) (default: False)

The following settings are recognized without a prepending flag:

add_based_on_distance_connectivity :: bool: Whether to add the connectivity (i.e. add bonds) as derived from atomic distances when graphs are generated. (default: True)
sub_based_on_distance_connectivity :: bool: Whether to subtract the connectivity (i.e. remove bonds) as derived from atomic distances when graphs are generated. (default: True)
only_distance_connectivity :: bool: Whether to impose the connectivity solely from distances. (default: False)
imaginary_wavenumber_threshold :: float: Threshold value in inverse centimeters below which a wavenumber is considered as imaginary when the transition state is analyzed. Negative numbers are interpreted as imaginary. (default: 0.0)
spin_propensity_check :: int: The range to check for possible multiplicities for products. A value of 2 (default) will check triplet and quintet for a singlet and will check singlet, quintet und septet for triplet.

Additionally all settings that are recognized by the SCF program chosen. are also available. These settings are not required to be prepended with any flag.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: molassembler (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful (technically and chemically) the following data will be generated and added to the database:

Elementary Steps: If found, a single new elementary step with the associated transition state will be added to the database.
Structures: The transition state (TS) and also the separated products will be added to the database.
Properties: The hessian (DenseMatrixProperty), frequencies (VectorProperty), normal_modes (DenseMatrixProperty), gibbs_energy_correction (NumberProperty) and gibbs_free_energy (NumberProperty) of the TS will be provided. The electronic_energy associated with the TS structure and each of the products will be added to the database.

SCINE: Single Point¶

class scine_puffin.jobs.scine_single_point.ScineSinglePoint[source]¶

A job calculating the electronic energy for a given structure with a given model.

Order Name

scine_single_point

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

All settings that are recognized by the program chosen.: Furthermore, all settings that are commonly understood by any program interface via the SCINE Calculator interface.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, i.e. Sparrow

Generated Data

If successful the following data will be generated and added to the database:

Properties: The electronic_energy associated with the given structure. The atomic_charges associated with the given structure (if available).

SCINE: Transition State Optimization¶

class scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization[source]¶

A job searching the nearest saddlepoint on the potential energy surface. Optimizing a given structure’s geometry, generating a new transition state structure, if successful.

Order Name

scine_ts_optimization

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

All settings recognized by ReaDuct’s transition state search

Common examples are:

optimizer :: str: The name of the optimizer to be used, e.g. ‘bofill’ or ‘evf’ or ‘dimer’.
convergence_max_iterations :: int: The maximum number of geometry optimization cycles.
convergence_delta_value :: float: The convergence criterion for the electronic energy difference between two steps.
convergence_gradient_max_coefficient :: float: The convergence criterion for the maximum absolute gradient. contribution.
convergence_step_rms :: float: The convergence criterion for root mean square of the geometric gradient.
convergence_step_max_coefficient :: float: The convergence criterion for the maximum absolute coefficient in the last step taken in the geometry optimization.
convergence_gradient_rms :: float: The convergence criterion for root mean square of the last step taken in the geometry optimization.

For a complete list see the ReaDuct manual

All settings that are recognized by the SCF program chosen.

Common examples are:

max_scf_iterations :: int: The number of allowed SCF cycles until convergence.

Required Packages

SCINE: Database (present by default)
SCINE: Readuct (present by default)
SCINE: Utils (present by default)
A program implementing the SCINE Calculator interface, e.g. Sparrow

Generated Data

If successful the following data will be generated and added to the database:

Structures: A new transition state structure.
Properties: The electronic_energy associated with the new structure.

Specialized Jobs¶

Gaussian: Partial Charges - Charge Model 5¶

class scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5[source]¶

A job calculating CM5 (Charge Model 5) atomic partial charges based on the Hirshfeld population analysis for a given structure with the Gaussian program.

Order Name

gaussian_charge_model_5

Optional Settings

There are no optional settings.

Required Packages

SCINE: Database (present by default)
SCINE: Utils (present by default)
The Gaussian program has to be available.

Generated Data

If successful the following data will be generated and added to the database:

Properties: The cm5_charges calculated for the given structure.

Orca: Geometry Optimization¶

class scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization[source]¶

A job optimizing the geometry of a given structure with the Orca program, in search of a local minimum on the potential energy surface. Optimizing a given structure’s geometry, generating a new minimum energy structure, if successful.

Order Name

orca_geometry_optimization

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

convergence_max_iterations :: int: The maximum number of geometry optimization cycles.
cartesian_constraints :: List[int]: A list of atom indices of the atoms which positions will be constrained during the optimization.
max_scf_iterations :: int: The number of allowed SCF cycles until convergence.
self_consistence_criterion :: float: The self consistence criterion corresponding to the maximum energy change between two SCF cycles resulting in convergence.
scf_damping :: bool: Switches damping on or off during the SCF by employing the Orca keyword SlowConv. The default is False.
calculate_hirshfeld_charges :: bool: Calculates atomic partial charges based on the Hirshfeld population analysis for the optimized structure and stores these into the database. The default is False.
transform_coordinates :: bool: Switch to transform the input coordinates from Cartesian to redundant internal coordinates. Setting this value to False and hence performing the calculation in Cartesian coordinates is helpful in rare occasions where the calculation with redundant internal coordinates fails. The optimization will take more time but is more likely to end successfully. The default is True.

Required Packages

SCINE: Database (present by default)
SCINE: Utils (present by default)
The Orca program has to be available

Generated Data

If successful the following data will be generated and added to the database:

Structures: A new minimum energy structure.
Properties: The electronic_energy associated with the new structure.

Turbomole: Geometry Optimization¶

class scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization[source]¶

A job optimizing the geometry of a given structure with the Turbomole program, in search of a local minimum on the potential energy surface. Optimizing a given structure’s geometry, generating a new minimum energy structure, if successful.

Order Name

turbomole_geometry_optimization

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

cartesian_constraints :: List[int]: A list of atom indices of the atoms which positions will be constrained during the optimization.
max_scf_iterations :: int: The number of allowed SCF cycles until convergence. Default value is 30.
transform_coordinates :: bool: Switch to transform the input coordinates from redundant internal to cartesian coordinates. Setting this value to True and hence performing the calculation in Cartesian coordinates is helpful in rare occasions where the calculation with redundant internal coordinates fails. The optimization will take more time but is more likely to end successfully. The default is False.
convergence_max_iterations :: int: The maximum number of geometry optimization cycles.
scf_damping :: bool: Increases damping during the SCF by modifying the $scfdamp parameter in the control file. The default is False.
scf_orbitalshift :: float: Shifts virtual orbital energies upwards. Default value is 0.1.
convergence_delta_value :: int: The convergence criterion for the electronic energy difference between two steps. The default value is 1E-6.
calculate_loewdin_charges :: bool: Calculates the Loewdin partial charges. The default is False.
self_consistence_criterion :: float: The self consistence criterion corresponding to the maximum energy change between two SCF cycles resulting in convergence. Default value ist 1E-6.
spin_mode :: string: Sets the spin mode. If no spin mode is set, Turbomole’s default for the corresponding system is chosen. Options are: restricted, unrestricted.

Required Packages

SCINE: Database (present by default)
SCINE: Utils (present by default)
The Turbomole program has to be available

Generated Data

If successful the following data will be generated and added to the database:

Structures: A new minimum energy structure.
Properties: The electronic_energy associated with the new structure and atomic_charges for all atoms, if requested.

Turbomole: Single Point¶

class scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint[source]¶

A job calculating the electronic energy for a given structure with the Turbomole program.

Order Name

turbomole_single_point

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

self_consistence_criterion :: float: The self consistence criterion corresponding to the maximum energy change between two SCF cycles resulting in convergence. Default value ist 1E-6.
cartesian_constraints :: List[int]: A list of atom indices of the atoms which positions will be constrained during the optimization.
max_scf_iterations :: int: The number of allowed SCF cycles until convergence. Default value is 30.
transform_coordinates :: bool: Switch to transform the input coordinates from redundant internal to cartesian coordinates. Setting this value to True and hence performing the calculation in Cartesian coordinates is helpful in rare occasions where the calculation with redundant internal coordinates fails. The optimization will take more time but is more likely to end successfully. The default is True.
scf_damping :: bool: Increases damping during the SCF by modifying the $scfdamp parameter in the control file. The default is False.
scf_orbitalshift :: float: Shifts virtual orbital energies upwards. Default value is 0.1.
calculate_loewdin_charges :: bool: Calculates the Loewdin partial charges. The default is False.
spin_mode :: string: Sets the spin mode. If no spin mode is set, Turbomole’s default for the corresponding system is chosen. Options are: restricted, unrestricted.

Required Packages

SCINE: Database (present by default)
SCINE: Utils (present by default)
The Turbomole program has to be available

Generated Data

If successful the following data will be generated and added to the database:

Properties

The electronic_energy associated with the structure. atomic_charges for all atoms, if requested.

Turbomole: Hessian¶

class scine_puffin.jobs.turbomole_hessian.TurbomoleHessian[source]¶

A job generating a Hessian and derived data for a single structure.

Order Name

turbomole_hessian

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

self_consistence_criterion :: float: The self consistence criterion corresponding to the maximum energy change between two SCF cycles resulting in convergence. Default value ist 1E-6.
cartesian_constraints :: List[int]: A list of atom indices of the atoms which positions will be constrained during the optimization.
max_scf_iterations :: int: The number of allowed SCF cycles until convergence. Default value is 30.
transform_coordinates :: bool: Switch to transform the input coordinates from redundant internal to cartesian coordinates. Setting this value to True and hence performing the calculation in Cartesian coordinates is helpful in rare occasions where the calculation with redundant internal coordinates fails. The optimization will take more time but is more likely to end successfully. The default is True.
scf_damping :: bool: Increases damping during the SCF by modifying the $scfdamp parameter in the control file. The default is False.
scf_orbitalshift :: float: Shifts virtual orbital energies upwards. Default value is 0.1.
calculate_loewdin_charges :: bool: Calculates the Loewdin partial charges. The default is False.
spin_mode :: str: Sets the spin mode. If no spin mode is set, Turbomole’s default for the corresponding system is chosen. Options are: restricted, unrestricted.

Required Packages

SCINE: Database (present by default)
SCINE: Utils (present by default)
The Turbomole program has to be available

Generated Data

If successful the following data will be generated and added to the database:

Properties: The hessian and the electronic_energy associated with the structure. atomic_charges for all atoms, if requested

Turbomole: Bond Orders¶

class scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders[source]¶

A job generating Wiberg bond orders and derived data for a single structure.

Order Name

turbomole_bond_orders

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

All settings that are recognized by the turbomole_single_point job.

Required Packages

SCINE: Database (present by default)
SCINE: Utils (present by default)
The Turbomole program has to be available

Generated Data

If successful the following data will be generated and added to the database:

Properties: The bond_orders and the electronic_energy associated with the structure.

Debugging: Sleep¶

class scine_puffin.jobs.sleep.Sleep[source]¶

A dummy job used for debug purposes. The job sleeps for a given amount of time.

Order Name

sleep

Optional Settings

Optional settings are read from the settings field, which is part of any Calculation stored in a SCINE Database. Possible settings for this job are:

time :: int: The time to sleep for in seconds. Default: 300.

Required Packages

SCINE: Database (present by default)

Generated Data

This dummy job does not generate new data.