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nebwork.py
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nebwork.py
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from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.base import Int, Str, Float, Bool
from aiida.orm.data.singlefile import SinglefileData
from aiida.orm.data.folder import FolderData
from aiida.orm.code import Code
from aiida.common.exceptions import NotExistent
# from aiida.orm.data.structure import StructureData
from aiida.work.workchain import WorkChain, ToContext, Calc, while_
from aiida.work.run import submit
from aiida_cp2k.calculations import Cp2kCalculation
class NEBWorkchain(WorkChain):
@classmethod
def define(cls, spec):
super(NEBWorkchain, cls).define(spec)
spec.input("cp2k_code", valid_type=Code)
spec.input("struc_folder", valid_type=FolderData)
spec.input("num_machines", valid_type=Int)
spec.input("calc_name", valid_type=Str)
spec.input("cell", valid_type=Str)
spec.input("fixed_atoms", valid_type=Str)
spec.input("nproc_rep", valid_type=Int)
spec.input("nreplicas", valid_type=Int)
spec.input("spring", valid_type=Float)
spec.input("rotate", valid_type=Bool)
spec.input("align", valid_type=Bool)
spec.input("nstepsit", valid_type=Int)
spec.input("endpoints", valid_type=Bool)
spec.input("calc_type", valid_type=Str)
spec.input("first_slab_atom", valid_type=Int)
spec.input("last_slab_atom", valid_type=Int)
spec.outline(
cls.init,
cls.calc_neb,
while_(cls.not_converged)(
cls.calc_neb
),
# cls.store_neb
)
spec.dynamic_output()
# ==========================================================================
def not_converged(self):
try:
self.report('Convergence check DEBUG: {}'.format(self.ctx.neb))
self.report('Convergence check: {}'
.format(self.ctx.neb.res.exceeded_walltime))
return self.ctx.neb.res.exceeded_walltime
except AttributeError:
return True
except NotExistent:
return False
# ==========================================================================
def init(self):
self.report('Init NEB')
# Set the restart folder
try:
self.ctx.remote_calc_folder = self.ctx.neb.remote_calc_folder
except AttributeError:
self.ctx.remote_calc_folder = None
# Here we need to create the xyz files of all the replicas
self.ctx.this_name = self.inputs.calc_name
self.ctx.file_list = self.inputs.struc_folder.get_folder_list()
self.ctx.n_files = len(self.ctx.file_list)-2
# Report some things
self.report('Passed #{} replica geometries'.format(self.ctx.n_files))
self.report('Replicas: {}'.format(self.ctx.file_list))
# ==========================================================================
def calc_neb(self):
self.report("Running CP2K CI-NEB calculation."
.format(self.ctx.this_name))
inputs = self.build_calc_inputs(self.inputs.struc_folder,
# Setup calculation
self.inputs.cell,
self.inputs.cp2k_code,
self.inputs.fixed_atoms,
self.inputs.num_machines,
self.ctx.remote_calc_folder,
# NEB input
self.inputs.align,
self.inputs.endpoints,
self.inputs.nproc_rep,
self.inputs.nreplicas,
self.inputs.nstepsit,
self.inputs.rotate,
self.inputs.spring,
# Calculation type specific
self.inputs.calc_type,
self.ctx.file_list,
# find this in the workflow
# instead of passing
self.inputs.first_slab_atom,
self.inputs.last_slab_atom)
self.report(" ")
self.report("inputs: "+str(inputs))
self.report(" ")
future = submit(Cp2kCalculation.process(), **inputs)
self.report("future: "+str(future))
self.report(" ")
return ToContext(neb=Calc(future))
# ==========================================================================
def store_replica(self):
return self.out('replica_{}'.format(self.ctx.this_name),
self.ctx.neb.out.output_structure)
# ==========================================================================
@classmethod
def build_calc_inputs(cls, struc_folder, cell, code,
fixed_atoms, num_machines, remote_calc_folder,
# NEB input
align, endpoints, nproc_rep, nreplicas, nstepsit,
rotate, spring,
# Calculation type specific
calc_type, file_list, first_slab_atom,
last_slab_atom):
inputs = {}
inputs['_label'] = "NEB"
inputs['code'] = code
inputs['file'] = {}
# The files passed by the notebook
for f in struc_folder.get_folder_list():
path = struc_folder.get_abs_path()+'/path/'+f
inputs['file'][f] = SinglefileData(file=path)
# Au potential
pot_f = SinglefileData(file='/project/apps/surfaces/slab/Au.pot')
inputs['file']['au_pot'] = pot_f
remote_computer = code.get_remote_computer()
machine_cores = remote_computer.get_default_mpiprocs_per_machine()
if 'Mixed' in str(calc_type):
# Then we have mol0.xyz which is not a replica itself
nreplica_files = len(file_list)-1
else:
nreplica_files = len(file_list)
if calc_type == 'Mixed DFTB':
walltime = 18000
else:
walltime = 86000
inp = cls.get_cp2k_input(cell=cell,
fixed_atoms=fixed_atoms,
machine_cores=machine_cores*num_machines,
# NEB input
align=align,
endpoints=endpoints,
nproc_rep=nproc_rep,
nreplicas=nreplicas,
nstepsit=nstepsit,
rotate=rotate,
spring=spring,
# Calculation specific
calc_type=calc_type,
nreplica_files=nreplica_files,
first_slab_atom=first_slab_atom,
last_slab_atom=last_slab_atom,
walltime=walltime*0.97)
if remote_calc_folder is not None:
inputs['parent_folder'] = remote_calc_folder
inputs['parameters'] = ParameterData(dict=inp)
# settings
settings = ParameterData(dict={'additional_retrieve_list': ['*.xyz',
'*.out',
'*.ener']})
inputs['settings'] = settings
# resources
inputs['_options'] = {
"resources": {"num_machines": num_machines},
"max_wallclock_seconds": walltime,
}
return inputs
# ==========================================================================
@classmethod
def get_cp2k_input(cls, cell, fixed_atoms, machine_cores,
align, endpoints, nproc_rep, nreplicas,
nstepsit, rotate, spring,
calc_type, nreplica_files,
first_slab_atom, last_slab_atom,
walltime):
inp = {
'GLOBAL': {
'RUN_TYPE': 'BAND',
'WALLTIME': walltime,
'PRINT_LEVEL': 'LOW'
},
'MOTION': cls.get_motion(align, endpoints, fixed_atoms, nproc_rep,
nreplicas, nstepsit, rotate, spring,
nreplica_files),
'FORCE_EVAL': [],
}
if calc_type == 'Mixed DFTB':
inp['FORCE_EVAL'] = [cls.force_eval_mixed(cell,
first_slab_atom,
last_slab_atom,
machine_cores),
cls.force_eval_fist(cell),
cls.get_force_eval_qs_dftb(cell)]
inp['MULTIPLE_FORCE_EVALS'] = {
'FORCE_EVAL_ORDER': '2 3',
'MULTIPLE_SUBSYS': 'T'
}
elif calc_type == 'Mixed DFT':
inp['FORCE_EVAL'] = [cls.force_eval_mixed(cell,
first_slab_atom,
last_slab_atom,
machine_cores),
cls.force_eval_fist(cell),
cls.get_force_eval_qs_dft(cell,
'mol0.xyz')]
inp['MULTIPLE_FORCE_EVALS'] = {
'FORCE_EVAL_ORDER': '2 3',
'MULTIPLE_SUBSYS': 'T'
}
elif calc_type == 'Full DFT':
# The right structure!
inp['FORCE_EVAL'] = [cls.get_force_eval_qs_dft(cell,
'replica1.xyz')]
return inp
# ==========================================================================
@classmethod
def force_eval_mixed(cls, cell, first_slab_atom, last_slab_atom,
machine_cores):
first_mol_atom = 1
last_mol_atom = first_slab_atom - 1
mol_delim = (first_mol_atom, last_mol_atom)
slab_delim = (first_slab_atom, last_slab_atom)
force_eval = {
'METHOD': 'MIXED',
'MIXED': {
'MIXING_TYPE': 'GENMIX',
'GROUP_PARTITION': '2 %d' % (machine_cores-2),
'GENERIC': {
'ERROR_LIMIT': '1.0E-10',
'MIXING_FUNCTION': 'E1+E2',
'VARIABLES': 'E1 E2'
},
'MAPPING': {
'FORCE_EVAL_MIXED': {
'FRAGMENT':
[{'_': '1', ' ': '%d %d' % mol_delim},
{'_': '2', ' ': '%d %d' % slab_delim}],
},
'FORCE_EVAL': [{'_': '1', 'DEFINE_FRAGMENTS': '1 2'},
{'_': '2', 'DEFINE_FRAGMENTS': '1'}],
}
},
'SUBSYS': {
'CELL': {'ABC': cell},
'TOPOLOGY': {
'COORD_FILE_NAME': 'replica1.xyz',
'COORDINATE': 'XYZ',
'CONNECTIVITY': 'OFF',
},
}
}
return force_eval
# ==========================================================================
@classmethod
def force_eval_fist(cls, cell):
ff = {
'SPLINE': {
'EPS_SPLINE': '1.30E-5',
'EMAX_SPLINE': '0.8',
},
'CHARGE': [],
'NONBONDED': {
'GENPOT': [],
'LENNARD-JONES': [],
'EAM': {
'ATOMS': 'Au Au',
'PARM_FILE_NAME': 'Au.pot',
},
},
}
for x in ('Au', 'H', 'C', 'O', 'N'):
ff['CHARGE'].append({'ATOM': x, 'CHARGE': 0.0})
genpot_fun = 'A*exp(-av*r)+B*exp(-ac*r)-C/(r^6)/( 1+exp(-20*(r/R-1)) )'
genpot_val = '4.13643 1.33747 115.82004 2.206825'\
' 113.96850410723008483218 5.84114'
for x in ('C', 'N', 'O', 'H'):
ff['NONBONDED']['GENPOT'].append(
{'ATOMS': 'Au ' + x,
'FUNCTION': genpot_fun,
'VARIABLES': 'r',
'PARAMETERS': 'A av B ac C R',
'VALUES': genpot_val,
'RCUT': '15'}
)
for x in ('C H', 'H H', 'H N', 'C C', 'C O', 'C N', 'N N', 'O H',
'O N', 'O O'):
ff['NONBONDED']['LENNARD-JONES'].append(
{'ATOMS': x,
'EPSILON': '0.0',
'SIGMA': '3.166',
'RCUT': '15'}
)
force_eval = {
'METHOD': 'FIST',
'MM': {
'FORCEFIELD': ff,
'POISSON': {
'EWALD': {
'EWALD_TYPE': 'none',
},
},
},
'SUBSYS': {
'CELL': {
'ABC': cell,
},
'TOPOLOGY': {
'COORD_FILE_NAME': 'replica1.xyz',
'COORDINATE': 'XYZ',
'CONNECTIVITY': 'OFF',
},
},
}
return force_eval
# ==========================================================================
@classmethod
def get_force_eval_qs_dftb(cls, cell):
force_eval = {
'METHOD': 'Quickstep',
'DFT': {
'QS': {
'METHOD': 'DFTB',
'EXTRAPOLATION': 'USE_GUESS',
'DFTB': {
'SELF_CONSISTENT': 'T',
'DISPERSION': 'T',
'ORTHOGONAL_BASIS': 'F',
'DO_EWALD': 'F',
'PARAMETER': {
'PARAM_FILE_PATH': 'DFTB/scc',
'PARAM_FILE_NAME': 'scc_parameter',
'UFF_FORCE_FIELD': '../uff_table',
},
},
},
'SCF': {
'MAX_SCF': '30',
'SCF_GUESS': 'RESTART',
'EPS_SCF': '1.0E-6',
'OT': {
'PRECONDITIONER': 'FULL_SINGLE_INVERSE',
'MINIMIZER': 'CG',
},
'OUTER_SCF': {
'MAX_SCF': '20',
'EPS_SCF': '1.0E-6',
},
'PRINT': {
'RESTART': {
'EACH': {
'QS_SCF': '0',
'GEO_OPT': '1',
},
'ADD_LAST': 'NUMERIC',
'FILENAME': 'RESTART'
},
'RESTART_HISTORY': {'_': 'OFF'}
}
}
},
'SUBSYS': {
'CELL': {'ABC': cell},
'TOPOLOGY': {
'COORD_FILE_NAME': 'mol0.xyz',
'COORDINATE': 'xyz'
}
}
}
return force_eval
# ==========================================================================
@classmethod
def get_motion(cls, align, endpoints, fixed_atoms, nproc_rep, nreplicas,
nstepsit, rotate, spring, nreplica_files):
motion = {
'CONSTRAINT': {
'FIXED_ATOMS': {
'LIST': '{}'.format(fixed_atoms)
}
},
'BAND': {
'NPROC_REP': nproc_rep,
'BAND_TYPE': 'CI-NEB',
'NUMBER_OF_REPLICA': nreplicas,
'K_SPRING': str(spring),
'CONVERGENCE_CONTROL': {
'MAX_FORCE': '0.0005',
'RMS_FORCE': '0.001',
'MAX_DR': '0.002',
'RMS_DR': '0.005'
},
'ROTATE_FRAMES': str(rotate)[0],
'ALIGN_FRAMES': str(align)[0],
'CI_NEB': {
'NSTEPS_IT': str(nstepsit)
},
'OPTIMIZE_BAND': {
'OPT_TYPE': 'DIIS',
'OPTIMIZE_END_POINTS': str(endpoints)[0],
'DIIS': {
'MAX_STEPS': 1000
}
},
'PROGRAM_RUN_INFO': {
'INITIAL_CONFIGURATION_INFO': ''
},
'CONVERGENCE_INFO': {
'_': ''
},
'REPLICA': []
},
}
# The fun part
for r in range(nreplica_files):
motion['BAND']['REPLICA'].append({
'COORD_FILE_NAME': 'replica{}.xyz'.format(r+1)
})
return motion
# ==========================================================================
@classmethod
def get_force_eval_qs_dft(cls, cell, coord_file_name):
force_eval = {
'METHOD': 'Quickstep',
'DFT': {
'BASIS_SET_FILE_NAME': 'BASIS_MOLOPT',
'POTENTIAL_FILE_NAME': 'POTENTIAL',
'RESTART_FILE_NAME': './parent_calc/aiida-RESTART.wfn',
'QS': {
'METHOD': 'GPW',
'EXTRAPOLATION': 'USE_GUESS',
'EPS_DEFAULT': '1.0E-14',
},
'MGRID': {
'CUTOFF': '600',
'NGRIDS': '5',
},
'SCF': {
'MAX_SCF': '20',
'SCF_GUESS': 'RESTART',
'EPS_SCF': '1.0E-7',
'OT': {
'PRECONDITIONER': 'FULL_SINGLE_INVERSE',
'MINIMIZER': 'CG',
},
'OUTER_SCF': {
'MAX_SCF': '50',
'EPS_SCF': '1.0E-7',
},
'PRINT': {
'RESTART': {
'EACH': {
'QS_SCF': '0',
'GEO_OPT': '1',
},
'ADD_LAST': 'NUMERIC',
'FILENAME': 'RESTART'
},
'RESTART_HISTORY': {'_': 'OFF'}
}
},
'XC': {
'XC_FUNCTIONAL': {'_': 'PBE'},
'VDW_POTENTIAL': {
'DISPERSION_FUNCTIONAL': 'PAIR_POTENTIAL',
'PAIR_POTENTIAL': {
'TYPE': 'DFTD3',
'CALCULATE_C9_TERM': '.TRUE.',
'PARAMETER_FILE_NAME': 'dftd3.dat',
'REFERENCE_FUNCTIONAL': 'PBE',
'R_CUTOFF': '[angstrom] 15',
}
}
},
},
'SUBSYS': {
'CELL': {'ABC': cell},
'TOPOLOGY': {
# starting geometry
'COORD_FILE_NAME': coord_file_name,
'COORDINATE': 'xyz',
},
'KIND': [],
}
}
force_eval['SUBSYS']['KIND'].append({
'_': 'Au',
'BASIS_SET': 'DZVP-MOLOPT-SR-GTH',
'POTENTIAL': 'GTH-PBE-q11'
})
force_eval['SUBSYS']['KIND'].append({
'_': 'C',
'BASIS_SET': 'TZV2P-MOLOPT-GTH',
'POTENTIAL': 'GTH-PBE-q4'
})
force_eval['SUBSYS']['KIND'].append({
'_': 'Br',
'BASIS_SET': 'DZVP-MOLOPT-SR-GTH',
'POTENTIAL': 'GTH-PBE-q7'
})
force_eval['SUBSYS']['KIND'].append({
'_': 'O',
'BASIS_SET': 'TZV2P-MOLOPT-GTH',
'POTENTIAL': 'GTH-PBE-q6'
})
force_eval['SUBSYS']['KIND'].append({
'_': 'N',
'BASIS_SET': 'TZV2P-MOLOPT-GTH',
'POTENTIAL': 'GTH-PBE-q5'
})
force_eval['SUBSYS']['KIND'].append({
'_': 'I',
'BASIS_SET': 'DZVP-MOLOPT-SR-GTH',
'POTENTIAL': 'GTH-PBE-q7'
})
force_eval['SUBSYS']['KIND'].append({
'_': 'H',
'BASIS_SET': 'TZV2P-MOLOPT-GTH',
'POTENTIAL': 'GTH-PBE-q1'
})
return force_eval