Source code for moldesign.parameters

# Copyright 2016 Autodesk Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

This module stores definitions of common parameters for common techniques.

These are used to standardize our interfaces to other codes, and automatically generate interactive
notebook interfaces to configure various techniques.
import operator as op

from moldesign import units as u
from moldesign import utils

[docs]def isin(a, b): return a in b
[docs]class WhenParam(object): def __init__(self, parameter, operator, checkval): self.operator = operator self.parameter = parameter self.checkval = checkval def __call__(self, paramset): """ Args: paramset (dict): Returns: bool: True if the parameter is releveant, false otherwise """ #TODO: anything relevant to an irrelevant parameter is also irrelevant return self.operator(paramset[self.parameter], self.checkval)
[docs]class Parameter(object): """ A generic parameter for a computational method Args: name (str): the arguments name (this is also its key in the method's ``params`` dictionary) short_description (str): A more readable description of about 100 characters type: The type of the param, including units if applicable. This may be a type (``int``, ``str``, etc.); if the quantity has physical units, you may also pass an example of this quantity (e.g., ``1.0 * units.angstrom``) default: the default value, or None if the user is required to set this parameter manually choices (list): A list of allowable values for the parameter help_url (str): URL for detailed help (not currently implemented) relevance (WhenParam): specifies when a given parameter will affect the dynamics Examples: >>> Parameter('timestep', 'Dynamics timestep', type=1.0*u.fs, default=2.0*u.fs) <Parameter "timestep", type: float, units: fs> >>> Parameter('functional', 'DFT XC functional', choices=['b3lyp', 'pbe0'], >>> relevance=WhenParam('theory', op.eq, 'rks')) <Parameter "functional", type: str> """ def __init__(self, name, short_description=None, type=None, default=None, choices=None, help_url=None, relevance=None): = name self.displayname = utils.if_not_none(short_description, name) self.value = None self.default = default self.choices = utils.if_not_none(choices, []) self.type = type self.help_url = help_url if isinstance(type, u.MdtQuantity): type = type.units if isinstance(type, u.MdtUnit): self.type = float self.units = type else: self.units = None self.relevance = relevance def __str__(self): s = '%s "%s", type: %s' % (type(self).__name__,, self.type.__name__) if self.units is not None: s += ', units: %s' % self.units return s def __repr__(self): try: return '<%s>' % self except: return '<%s at %x - exc in __repr__>' % (type(self), id(self))
# TODO - make this ordered as well as dotted
[docs]def named_dict(l): return utils.OrderedDotDict((, i) for i in l)
model_parameters = named_dict([ Parameter('subsystem') ]) FORCEFIELDS = [] PERIODICITIES = [False, 'box'] mm_model_parameters = named_dict([ Parameter('cutoff', 'Cutoff for nonbonded interactions', default=1.0*u.nm, type=u.nm), Parameter('nonbonded', 'Nonbonded interaction method', default='cutoff', type=str, choices=['cutoff', 'pme', 'ewald']), Parameter('implicit_solvent', 'Implicit solvent method', type=str, choices=['gbsa', 'obc', 'pbsa', None]), Parameter('solute_dielectric', 'Solute dielectric constant', default=1.0, type=float), Parameter('solvent_dielectric', 'Solvent dielectric constant', default=78.5, type=float), Parameter('ewald_error', 'Ewald error tolerance', default=0.0005, type=float), Parameter('periodic', 'Periodicity', default=False, choices=PERIODICITIES) ]) QMTHEORIES = ['rhf', 'rks', 'mp2', 'casscf', 'casci', 'fci'] BASISSETS = ['3-21g', '4-31g', '6-31g', '6-31g*', '6-31g**', '6-311g', '6-311g*', '6-311g+', '6-311g*+', 'sto-3g', 'sto-6g', 'minao', 'weigend', 'dz' 'dzp', 'dtz', 'dqz', 'aug-cc-pvdz', 'aug-cc-pvtz', 'aug-cc-pvqz'] FUNCTIONALS = ['b3lyp', 'blyp', 'pbe0', 'x3lyp', 'mpw3lyp5'] # This is a VERY limited set to start with; all hybrid functionals for now # Need to think more about interface and what to offer by default # PySCF xcs are at for now qm_model_parameters = named_dict([ Parameter('theory', 'QM theory', choices=QMTHEORIES), Parameter('functional', 'DFT Functional', default='b3lyp', choices=FUNCTIONALS, # TODO: allow separate x and c functionals relevance=WhenParam('theory', isin, 'dft rks ks uks'.split())), Parameter('active_electrons', 'Active electrons', type=int, default=2, relevance=WhenParam('theory', isin, ['casscf', 'mcscf', 'casci'])), Parameter('active_orbitals', 'Active orbitals', type=int, default=2, relevance=WhenParam('theory', isin, ['casscf', 'mcscf', 'casci'])), Parameter('state_average', 'States to average for SCF', type=int, default=1, relevance=WhenParam('theory', isin, ['casscf', 'mcscf'])), Parameter('basis', 'Basis set', choices=BASISSETS), Parameter('wfn_guess', 'Starting guess method', default='huckel', choices=['huckel', 'minao', 'stored']), Parameter('store_orb_guesses', 'Automatically use orbitals for next initial guess', default=True, type=bool), Parameter('multiplicity', 'Spin multiplicity', default=1, type=int), Parameter('symmetry', 'Symmetry detection', default=None, choices=[None, 'Auto', 'Loose']), Parameter('initial_guess', 'Wfn for initial guess', relevance=WhenParam('wfn_guess', op.eq, 'stored')) ]) integrator_parameters = named_dict([ Parameter('timestep', 'Dynamics timestep', default=1.0*u.fs, type=u.default.time), Parameter('frame_interval', 'Time between frames', default=1.0*, type=u.fs) ]) md_parameters = named_dict([ Parameter('remove_translation', 'Remove global translations', default=True, type=bool), Parameter('constrain_hbonds', 'Constrain covalent hydrogen bonds', default=True, type=bool), Parameter('constrain_water', 'Constrain water geometries', default=True, type=bool), Parameter('remove_rotation', 'Remove global rotations', default=False, type=bool), ]) constant_temp_parameters = named_dict([ Parameter('temperature', 'Thermostat temperature', default=298 * u.kelvin, type=u.default.temperature)]) langevin_parameters = named_dict([ Parameter('collision_rate', 'Thermal collision rate', default=1.0/, type=1/ ]) ground_state_properties = ['potential_energy', 'forces', 'dipole_moment', 'quadrupole_moment', 'octupole_moment', 'mulliken_charges', 'esp_charges', 'orbitals', 'orbital_energies', 'ci_vector', 'hessian', 'am1_bcc_charges'] """If you're just calculating these, then just pass the requested quantities as a list of keywords to the calculate method""" excited_state_properties = ['state_energies', 'state_forces', 'state_ci_vector'] """ When requesting these quantities, requests need to be passed to mol.calculate as a dict with a list of states for each quantity, e.g. >>> mol.calculate(requests={'state_energies':[1,2],'forces':[1,2]}) to get state_energies and forces for states 1 and 2. Adiabatic states are indexed starting at 0, so state 0 is the ground state, 1 is the first excited state, etc. E.g.. state_energies[0] == potential_energy """ multistate_properties = ['transition_dipole', 'nacv', 'oscillator_strength'] """ When requesting these quantities, requests need to be passed to mol.calculate as a dict with a list of *pairs* of states for each quantity, e.g. >>> mol.calculate(requests={'esp_charges':None, 'nacv':[(0,1),(0,2),(1,2)]}) """