8.3.1.2. ReaxFF

The ReaxFFParameters class provides a parameterizable interface to the ReaxFF reactive force field. It can be initialized by passing a force field path to the constructor:

ff = ReaxFFParameters('path/to/ffield.ff')

By default, all relevant parameters will be marked as is_active==True (i.e. marked for parameterization). See the API for parameter naming conventions.

See also

8.3.1.2.1. Reading Legacy params Files

Outside of the ParAMS formalism, a params file is common to mark a set of paramters for optimization, and set their respective ranges. Support for these files is implemented in the ReaxFFParameters.read_paramsfile() method:

ff = ReaxFFParameters('path/to/ffield.ff')
ff.read_paramsfile('path/to/params')

The method will mark all matching parameters as is_active=True (and deactivate all remaining ones). Will raise an error if blocks that are not present in the force field are referenced in the params file. Note that the 4th column in the params file (delta value) will be ignored.

8.3.1.2.2. Addition of Parameters

The ReaxFF interface allows for the addition of new parameters through the add_blocks() method.

8.3.1.2.3. Trim (remove elements) from a ReaxFF force field

Use the trim() method.

8.3.1.2.5. Parameter Databases and Value Suggestions

The class can suggest suitable parameter values for a number of queried parameters. See the ReaxFFParameters.params_from_db() method for more information. By default, all force fields in $AMSHOME/atomicdata/ForceFields/ReaxFF will be used to return suggestions. Users can create their own databases from fewer (or more) force fields through the ReaxFFParameters.generate_paramsdb() method.

8.3.1.2.6. ReaxFF Conversion Functions

Outside of ParAMS, ReaxFF is parameterized with a training set defined in trainset.in and geo files. There are two functions available to help with the conversion to the ParAMS format:

trainset_to_params(trainsetfile, use_weights=True, default_sigmas=None) → DataSet

Converts a ReaxFF trainset.in file to a DataSet object.

Parameters:

trainsetfilestr

Path to trainset.in.

use_weightsbool

If False, all weights will be set to 1.0, and Sigma will be set to the value from trainset.in

If True, then new_weight/(new_sigma**2) == 1/(value_from_trainset_in**2).

new_sigma is taken from the standard Sigma value for the pertinent extractor, or from the default_sigmas dictionary.

default_sigmasdict

A dictionary of the type

{ ‘energy’: sigma_energy, ‘forces’: sigma_forces, ‘charges’: sigma_charges, ‘angles’: sigma_angles,

‘distance’: sigma_distance, ‘dihedral’: sigma_dihedral }

The sigma values should be given in the classic ReaxFF units, so kcal/mol for energy, angstrom for distance, etc.

The sigma values are taken from this dictionary only if use_weights == True

Returns:

ds : DataSet instance

geo_to_params(geofile: str, normal_run_settings: Settings | str) → JobCollection

Convert a ReaxFF geo file to a JobCollection instance.

  • Each entry’s ID will be based on the DESCRP line. Duplicates will not be added.

  • Will guess the settings for each job based on the RUTYPE line. Can either be SinglePoint or GeometryOptimization (optionally with MaxIterations).

Parameters:

geofilestr

Path to geo file.

normal_run_settingsplams.Settings, str

A plams.Settings instance representing the NORMAL RUN or the path to a control file from which the settings will be extracted

Returns:

jc : JobCollection

8.3.1.2.7. ReaxFF Interface API

class ReaxFFParameters(ffieldfile, bounds_scale=1.2, settings=None)

Interface to the ReaxFF force field format.

Attributes:

In addition to the ones already availabe in BaseParameters

headerdict

A dictionary with metadata. header[‘head’] contains the first line of the force field

pathstr

The path to the last written ffield file.

blocksList[str]

Strings that mark valid parameter blocks. See ReaxFF manual for more information.

Note

This is a class attribute, meaning that an instance can contain fewer blocks.

allnamesDict[strList[str]]

A dictionary with BLOCK_NAME:List[PARAMETER_NAMES], where BLOCK_NAME is one of the elements from blocks. See also name_to_index() and names_in_block().

Note

This is a class attribute, meaning that an instance can contain fewer parameters.

shapeDict[strList[int]]

A dictionary of BLOCK_NAME:[NBLOCKS, N_PARAMS_IN_BLOCK], where BLOCK_NAME is one of the elements from blocks, NBLOCKS is the number of BLOCK_NAME blocks and N_PARAMS_IN_BLOCK is the number of parameters per block. See ReaxFF manual for more information.

flagsdict[str, str]

This attribute stores flags for special force field flavours. The data is read from the first line of the force field file, if it starts with [ X ], where X is a series of flag strings. Currently, the following flags are understood: ereaxff, ereaxff2, acks2, lgDispersion.

Parameter Naming Conventions:

Naming follows the tables as documented in the ReaxFF manual.
The name string is generated from the table’s Name in Eq column.
All atom-specific parameter names will start with the atom prefix, followed by the name: At1.At2.At3:NAME. For example, the name of the first parameter in the atoms block for a Hydrogen will be H:r_0^sigma.
See below for a full list of names.
Each parameter in the ReaxFF interface has the following additional attributes: block, block_index, equation, description, atoms_reversible. For easy filitering of parameters, see get(). For conversions between block indices and name strings, see the blocks, name_to_index() and names_in_block().

class Parameter(block, block_index, atoms, bounds_scale=0, *a, **kw)
__init__(block, block_index, atoms, bounds_scale=0, *a, **kw)
__init__(ffieldfile, bounds_scale=1.2, settings=None)

Initialize the class instance, reading a ffied from ffieldfile.

Parameters:

ffieldfilestr

Path to the force field file.

bounds_scalefloat >= 0

Apply arbitrary bounds, by providing a factor which will determine lower/upper bounds by b = x0 ± (bounds_scale-1)*abs(x0).

Note

Bounds for any x0 == 0 will be set to +-1.

settingsoptional, Settings

A plams.Settings instance that will be added to the output of get_engine(). Must have the input.ReaxFF keys defined.

__str__()

String representation of self

get_engine(parameters=None, path=None, write=True)

Note

When called without path, will store a ffield file in a temporary directory for as long as the returned Engine instance is referenced.

Returns:

A ReaxFF Engine class matching the passed params, or the current set of parameters if None.

write(file=None, parameters=None)

Writes the current parameters to file.

Note

When called without file, will store the ffield file in a temporary directory.
Use the path attribute to get the file path.

get_constraints() → List[Constraint]

Returns a list of physically reasonable Constraints for this instance to be passed to the Optimization.

Will constrain the covalent radii and bond lengths \(r_0\) for the \(\sigma, \pi, \pi\pi\) bonds to \(r_0^\sigma >= r_0^\pi >= r_0^\pi\pi\) and the Van der Waals radius \(r_\mathrm{VdW}\) to \(r_\mathrm{VdW}\) >= r_0^sigma`.

read_paramsfile(paramsfile)

Reads a legacy params file, sets all matching parameters to is_active=True (i.e. flags them as paramters to be fitted), and adjusts each parameter’s ranges to the ones from paramsfile.

add_blocks(params: List[str], allow_duplicates=False)

Adds new parameters to the current instance.
The addition happens block-wise by providing a list of strings, where each string represents the addition of one block. Strings must have the form At1.At2.At3.At4, where At represents the chemical symbol of the desired element (separated by dots) and the number of elements determines the block to be added (1 for the atomic block, 2 for bonds, 3 for angles, 4 for torsions). For example,

>>> ffield.add_blocks(['C.O', 'C.O.H'])

adds the C-O bonds block and the C-O-H angles block to the ffield instance. Off-diagonals and hydrogen-bonds can be added by prefixing a string with OFD: and HBD: respectively:

>>> ffield.add_blocks(['OFD:C.O', 'HBD:O.H.C'])

The above will add the C-O off-diagonal and O-H-C hydrogen-bond block.

Note

The following is of note when adding new blocks:

  • The addition of multiatomic blocks to a force field that does not yet contain all respective elements will automatically add the atomic block for that element. E.g., the addition of C-O to a force field that does not yet contain parameters for oxygen also implies the addition of O

  • Parameters added by this method have a value of 0. and a range of (-1, 1)

  • Already present blocks will not be overwritten, however, a duplicate block can be added by setting allow_duplicates=True

classmethod generate_paramsdb(paths=['$AMSHOME'], dbfile='reaxffdb.gz')

Generates a parameter database based on all force field files found in paths and stores it in dbfile.

Parameters:

pathsList[str]

When generating the database, each entry in paths can be either a directory, or a full path to a force field file. If a directory, will scan recursively and consider all files with the .ff ending.

dbfileoptional, str

Stores the generated database in dbfile. Defaults to reaxffdb.gz.

classmethod params_from_db(params: List[str], dbfile=None, **subst_atoms) → List[namedtuple]

Given a list of n parameter queries in params, scans a force field database stored in dbfile and returns n named tuples, which hold all parameters matching the query.

Properties:

paramsList[str]

Scans the data base for all entries in params. Each element is a string with either of the following syntaxes:

  • ‘BLOCK:At1.At2.At3.At4:INDEX’ or

  • ‘At1.At2.At3.At4:NAME’

where At1.At2.At3.At4 are chemical symbols (one to four). For the general block, this is replaced by None.

In the former case, BLOCK has to be any of {‘GEN’, ‘ATM’, ‘BND’, ‘OFD’, ‘ANG’, ‘TOR’, ‘HBD’} referring to the General, Atoms, Bonds, Off-Diagonals, Angles, Torsions, Hydrogen-Bonds blocks respectively. And INDEX is an integer specifying the parameter number for the block (starting with 0).

In the latter case, NAME refers to the string name of the desired parameter, following the same naming as in the names attribute (see Full List of Parameter Names).

dbfile: optional, str

Path to the database file to be used for the search. Defaults to a database generated from $AMSHOME/atomicdata/ForceFields/ReaxFF. See generate_paramsdb() for more information.

subst_atoms: optional keywords

Additional keywords will be interpreted as chemical elements (keys) that can be substitued by a number of other elements (values). This extends each query by matching all valid combinations of chemical elements for a specific parameter, rather than limiting it to one specific set of elements. Useful when queries should also include chemically similar elements.

Example:

>>> cls.params_from_db(['BND:C.O:0'], C=('Si', 'Ge'), O=('S',))

Will search all first entries of the bonds block considering the follwing combinaitons of elements: C.O, C.S, Ge.O, G.S, Si.O, Si.S.

Returns:

Returns a list of named 4-tuples. Each element in the list corresponds to a query. Each named tuple unpacks to (query, parametername, values, atoms, sources). Elements within the tuple are stored in the respective attribute (e.g. tup.values).

querystr

String used for the query, Same as in params

parameternamestr

String with the requested parameter’s name (excluding the chemical symbols prefix)

valuesarray

Array of all parameter values matching the query

atomsarray of str

Array of chemical elements corresponding to each returned parameter value

sourcesarray of str

Array of force field paths corresponding to the origin of each parameter value

classmethod block_from_db(block: str, dbfile=None)
blockstr

Should include the atoms. ‘GEN’, ‘BND:C.Cl’, ‘ANG:C.C.H’, etc.

dbfile: optional, str

Path to the database file to be used for the search. Defaults to a database generated from $AMSHOME/atomicdata/ForceFields/ReaxFF. See generate_paramsdb() for more information.

Returns a 2-tuple containing a dictionary and a list of parameter names. The keys of the dictionary are the sources (paths to .ff files), and the values are lists of parameter values.

names_in_block(block: str | int, atoms: str = '') → List[str]

Returns the names of the all parameters in block, optionally prepended by an {atoms}: string. block can either be a an int in the range of [0, 6] or any of {‘GEN’, ‘ATM’, ‘BND’, ‘OFD’, ‘ANG’, ‘TOR’, ‘HBD’} referring to the General, Atoms, Bonds, Off-Diagonals, Angles, Torsions, Hydrogen-Bonds blocks respectively.

Note

Index numbering starts from zero

See also

block_to_names()

classmethod name_to_index(name: str, block_as='str') → Tuple[int | str, int]

Given a parameter name, returns the indices at which this name is located within the force field blocks. The name argument should be a string of At1.At2:NAME, where At are the atoms (one to four) the parameter affects.
If block_as==’str’, the returned value is a (str, int), otherwise (int, int), where the first element specifies the block and the second one the index at which this is parameter located within the block. Blocks are represented by an int in the range of [0, 6] or strings of {‘GEN’, ‘ATM’, ‘BND’, ‘OFD’, ‘ANG’, ‘TOR’, ‘HBD’} referring to the General, Atoms, Bonds, Off-Diagonals, Angles, Torsions, Hydrogen-Bonds blocks respectively.

Note

Index numbering starts from zero.

copy_block(other_interface: ReaxFFParameters, from_block: str, to_block: str | None = None, copy_range: bool = True, allow_duplicates=False)

Copies the values (and optionally ranges) of a whole parameter block from other_interface to this instance.

Parameters:

other_ff: ReaxFFParameters

Copy the parameters in the block from this other instance

from_block: str

‘BND:C.C’ or similar. It is also possible to copy the complete block, _i.e._ all values in ‘BND’ or ‘OFD’ by passing only the three-letter block name.

to_blockstr or None

‘BND:C.O’ or similar. If None, set to the same value as from_block

copy_range: bool

Whether to copy the .range attribute from the other interface

get(name: str | None = None, atoms: str | None = None, block: str | int | None = None, index: int | None = None) → List[Parameter]

Returns a list of parameters in self based on a set of filters. Filtering can be based on:

Parameters:

namestr

Match a all parameters with name. Can be exact in the form of At1.At2:NAME, where At are the atoms for a parameter, or fuzzy in the form of NAME, meaning that all paraemters with NAME (regardless of atoms) will be matched

atomsstr

A string of the form ‘C.H’, ‘C.C.H’, etc

blockstr or int

Parameter block name (str) or index (int), matching :attr:blocks

indexint

The parameter at index within a block.

trim(keepatoms: List[str] | None = None)

Returns a new ReaxFFParameters instance, only keeping parameters describing interactions between atoms in the keepatoms list.

keepatoms: list of str

Elements to keep, e.g. [‘C’, ‘H’] or [‘C’, ‘H’, ‘0’]

NOTE: to save wildcard parameters, you need to explicitly include ‘0’ as one of the keepatoms.

Example:

>>> old = ReaxFFParameters('CHON2017_weak_bb.ff')
>>> new_interf = old.trim(keepatoms=['C', 'H', 'O'])

will keep the GEN block, ATM:C, …, BND:C.H, …., ANG:C.C.H, …., etc.

apply_default_constraints(only_active: bool = False, verbose: bool = False, parameter_names: List[str] | None = None)

Changes the parameter values and ranges to agree with the default constraints.

Example: Below the p_bo4 parameter is set to a value greater than or equal to 1.

>>> ff = ReaxFFParameters('CHO.ff')
>>> p = ff['H.H:p_bo4']
>>> p.is_active = True
>>> print(p.value, p.range, p.is_active)
0.0 [-1.0, 1.0] True
>>> ff.apply_default_constraints(only_active=True)
>>> print(p.value, p.range, p.is_active)
1.0 [1.0, 1.0] True

The following values/ranges will be altered:

('ATM', 'alpha_ij') >= 0
('OFD', 'alpha_ij') >= 0
('ATM', 'D_ij') >= 0
('OFD', 'D_ij', >= 0
('ATM', 'p_boc3') >= 0
('ATM', 'p_boc4') >= 0
('ATM', 'p_boc5') >= 0
('ATM', 'r_0^sigma') >= 0
('OFD', 'r_0^sigma') >= 0
('ATM', 'r_vdW') >= 0
('ATM', 'gamma_i') >= 0
('ATM', 'Val_i^e') >= 0
('BND', 'D_e^pi') >= 0
('BND', 'D_e^pipi') >= 0
('BND', 'D_e^sigma') >= 0
('BND', "Val'_i^boc") >= 0
('BND', 'p_be2') >= 0
('BND', 'p_ovun1') >= 0
('ANG', 'Theta_0,0') >= 0
('ANG', 'p_val2') >= 0
('ANG', 'p_val7') >= 0
('HBD', 'r_hb^0') >= 0

('ATM', '1/gamma_w') > 0.5

('BND', 'p_bo6') >= 1
('BND', 'p_bo4') >= 1
('BND', 'p_bo2') >= 1
('ANG', 'p_val4') >= 1

('ANG', 'Theta_0,0') < 180
only_active: bool

If True, make changes only to the active parameter subset

verbose: bool

Prints all changed parameters and the reason for changing them to stdout

parameter_names: list of str

Names of the parameters to apply default constraints to. If not set, all parameters will be considered. Note: the value of only_active is still considered.

get_default_constraints(only_active=True)

Returns a list of constraints that can be used in the input Constraints block in ParAMS (if each entry is separated by a newline).

only_activebool

Whether to only give constraints for the active subset.

classmethod yaml_load(yamlfile, *a, **kw)

Loads a parameter interface from a (compressed) human-readable yamlfile. Child classes should call super() in this method before implementing their own routines.

8.3.1.2.8. Full List of Parameter Names

General block, no prefix

  1. p_boc1

  2. p_boc2

  3. -p_coa2

  4. p_trip4

  5. p_trip3

  6. k_c2

  7. p_ovun6

  8. p_trip2

  9. p_ovun7

  10. p_ovun8

  11. p_trip1

  12. nonb_low,swa

  13. R_cut

  14. p_fe1

  15. p_val6

  16. p_lp1

  17. p_val9

  18. p_val10

  19. p_fe2

  20. p_pen2

  21. p_pen3

  22. p_pen4

  23. p_fe3

  24. p_tor2

  25. p_tor3

  26. p_tor4

  27. p_elho only if eReaxFF is enabled

  28. p_cot2

  29. p_vdW1

  30. cutoff*100

  31. p_coa4

  32. p_ovun4

  33. p_ovun3

  34. p_val8

  35. X_soft

  36. n/a 1

  37. p_val only if eReaxFF is enabled

  38. n/a 2

  39. p_coa3

  40. n/a 3

  41. n/a 4 only if eReaxFF is enabled

Atoms block, prefix: At1:

  1. r_0^sigma

  2. Val_i

  3. n/a 1

  4. r_vdW

  5. D_ij

  6. gamma_i

  7. r_0^pi

  8. Val_i^e

  9. alpha_ij

  10. 1/gamma_w

  11. Val_j^angle

  12. p_ovun5

  13. p_i^xel2 only if eReaxFF is enabled

  14. chi_i

  15. eta_i

  16. n/a 2

  17. r_0^pipi

  18. p_lp2

  19. n/a 3

  20. p_boc4

  21. p_boc3

  22. p_boc5

  23. C_i

  24. alpha_i only if eReaxFF is enabled

  25. p_ovun2

  26. p_val3

  27. beta_i only if eReaxFF is enabled

  28. Val_i^'boc

  29. p_val5

  30. p_c1

  31. p_c2

  32. p_c3

  33. C_i only if Lg dispersion is enabled

  34. R_eij only if Lg dispersion is enabled

Bonds block, prefix: At1.At2: (equivalent to At2.At1:)

  1. D_e^sigma

  2. D_e^pi

  3. D_e^pipi

  4. p_be1

  5. p_bo5

  6. Val'_i^boc

  7. p_bo6

  8. p_ovun1

  9. p_be2

  10. p_bo3

  11. p_bo4

  12. n/a

  13. p_bo1

  14. p_bo2

  15. delta'_i

  16. p_ij^xel1 only if eReaxFF is enabled

Off-diagonals block, prefix: At1.At2: (equivalent to At2.At1:)

  1. D_ij

  2. r_vdW

  3. alpha_ij

  4. r_0^sigma

  5. r_0^pi

  6. r_0^pipi

  7. C_i,C_lg,ij only if Lg dispersion is enabled

Angles block, prefix At1.At2.At3: (equivalent to At3.At2.At1, At2 is the central atom)

  1. Theta_0,0

  2. p_val1

  3. p_val2

  4. p_coa1

  5. p_val7

  6. p_pen1

  7. p_val4

Torsions block, prefix At1.At2.At3.At4: (equivalent to At4.At3.At2.A1:)

  1. V_1

  2. V_2

  3. V_3

  4. p_tor1

  5. p_cot1

  6. n/a 1

  7. n/a 2

Hydrogen Bonds block, prefix At1.H.At2: (NOT equivalent to At2.H.At1:)

  1. r_hb^0

  2. p_hb1

  3. -p_hb2

  4. -p_hb3

8.3.1.2.9. Parameter Categories

To guide your selection we have split the ReaxFF parameters into three categories:

  1. Standard: Parameters which are generally safe to optimize.

  2. Expert: Parameters which require some expert knowledge/insight. Generally, these are parameters which should be handled with more care and should only be tuned at the end of the parametrization process, if at all.

  3. DoNotOptimize: Parameters which should never be activated and changed through optimization. This final category generally represents parameters which act as boolean flags or switches, are not used by the force field, or contain physical constants like atomic mass.

Please note that these categorizations are entirely empirical and based only on in-house experience and expert knowledge. They are not definitive groupings, and serve only to better inform and guide your own decisions.

The category for each ReaxFF parameter is shown in a separate column of the GUI. When scripting it can be accessed via the metadata attribute of the Parameter class e.g. p.metadata.category or p.metadata['category'].