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Merge pull request MolSSI#158 from sjrl/entos_json
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Entos Update
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@dgasmith
dgasmith authored Sep 27, 2019
2 parents f63e481 + a818bf1 commit 0905f2e
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Showing 3 changed files with 160 additions and 47 deletions.
203 changes: 157 additions & 46 deletions qcengine/programs/entos.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,19 @@
"""

import string
from typing import Any, Dict, List, Optional, Tuple
import json
from typing import Any, Dict, List, Optional, Set, Tuple

from qcelemental.models import Result
from qcelemental.util import parse_version, safe_version, which

from ..exceptions import UnknownError
from ..exceptions import InputError, UnknownError
from ..util import execute, popen
from .model import ProgramHarness


class EntosHarness(ProgramHarness):
_defaults = {
_defaults: Dict[str, Any] = {
"name": "entos",
"scratch": True,
"thread_safe": False,
Expand All @@ -24,6 +25,27 @@ class EntosHarness(ProgramHarness):
}
version_cache: Dict[str, str] = {}

# Energy commands that are currently supported
_energy_commands: Set[str] = {"dft",
# "xtb"
}

# List of DFT functionals
_dft_functionals: Set[str] = {
"SLATER", "DIRAC", "SLATERD3", "DIRACD3", "VWN5", "VWN", "VWN1", "SVWN", "LDA", "BLYP", "BPW91",
"BLYPD3", "B88", "PBEX", "PBERX", "PBEC", "LYP", "PW91", "P86", "PBE", "PBER", "PBED3", "PBERD3",
"B3LYP3", "B3LYP", "B3LYP5", "PBE0", "PBE1PBE", "B3LYP3D3", "B3LYPD3", "B3LYP5D3", "PBE0D3",
"PBE1PBED3", "CAMB3LYP", "WB97X", "CAMB3LYPD3", "WB97XD3"
}

# Available keywords for each of the energy commands
_dft_keywords: Set[str] = {"df"}
# _xtb_keywords = {}
_keyword_map: Dict[str, Any] = {
"dft": _dft_keywords,
# "xtb": _xtb_keywords
}

class Config(ProgramHarness.Config):
pass

Expand All @@ -49,7 +71,7 @@ def compute(self, input_data: 'ResultInput', config: 'JobConfig') -> 'Result':
self.found(raise_error=True)

# Check entos version
if parse_version(self.get_version()) < parse_version("0.5"):
if parse_version(self.get_version()) < parse_version("0.6"):
raise TypeError("entos version '{}' not supported".format(self.get_version()))

# Setup the job
Expand Down Expand Up @@ -85,7 +107,7 @@ def execute(self,
infiles.update(extra_infiles)

# Collect all output files and extend with with extra_outfiles
outfiles = ["dispatch.out"]
outfiles = ["dispatch.out", "results.json"]
if extra_outfiles is not None:
outfiles.extend(extra_outfiles)

Expand All @@ -104,7 +126,7 @@ def execute(self,
timeout=timeout)

# Entos does not create an output file and only prints to stdout
proc["outfiles"]["dispatch.out"] = proc["stdout"]
proc["outfiles"]["results.json"] = proc["stdout"]
return exe_success, proc

def build_input(self, input_model: 'ResultInput', config: 'JobConfig',
Expand All @@ -113,28 +135,71 @@ def build_input(self, input_model: 'ResultInput', config: 'JobConfig',
# Write the geom xyz file with unit au
xyz_file = input_model.molecule.to_string(dtype='xyz', units='Angstrom')

# Create input dictionary
# Create input file
if template is None:
structure = {'structure': {'file': 'geometry.xyz'}}
dft_info = {
'xc': input_model.model.method,
'ao': input_model.model.basis.upper(),
'df_basis': input_model.keywords["df_basis"].upper(),
'charge': input_model.molecule.molecular_charge

# Determine the energy_command
energy_command = self.determine_energy_command(input_model.model.method)

# Define base options for the energy command (options that can be taken directly from input_model)
# TODO Perhaps create a new function that takes as input the energy command and
# returns the Dict energy_options
energy_options = {
"dft": {
'xc': input_model.model.method.upper(),
'ao': input_model.model.basis,
'charge': input_model.molecule.molecular_charge,
'spin': float(input_model.molecule.molecular_multiplicity - 1),
},
# "xtb": {}
}
print_results = {'print': {'results': True}}

# Resolve keywords (extra options) for the energy command
caseless_keywords = {k.lower(): v for k, v in input_model.keywords.items()}
energy_extra_options = {}
for key in caseless_keywords.keys():
if key in self._keyword_map[energy_command]:
energy_extra_options[key] = caseless_keywords[key]

# Additional sub trees
structure = {'structure': {'file': 'geometry.xyz'}} # Structure sub tree
print_results = {'print': {'results': True}} # Print sub tree
name_results = {'name': 'json_results'}

# Create the input dictionary for a energy call
if input_model.driver == 'energy':
input_dict = {'dft': {**structure, **dft_info}, **print_results}
# Write gradient call if asked for
input_dict = {
energy_command: {
**structure,
**energy_options[energy_command],
**energy_extra_options,
**name_results
},
**print_results,
}
# Create the input dictionary for a gradient call
elif input_model.driver == 'gradient':
input_dict = {'gradient': {**structure, 'dft': {**dft_info}}, **print_results}
input_dict = {
'gradient': {
**structure,
energy_command: {
**energy_options[energy_command],
**energy_extra_options
},
**name_results
},
**print_results,
}
# TODO Add support for hessians
# elif input_model.driver == 'hessian':
else:
raise NotImplementedError('Driver {} not implemented for entos.'.format(input_model.driver))
raise NotImplementedError(f'Driver {input_model.driver} not implemented for entos.')

# Write input file
input_file = self.write_input_recursive(input_dict)
input_file = "\n".join(input_file)

# Use the template input file if present
else:
# Some of the potential different template options
# (A) ordinary build_input (need to define a base template)
Expand All @@ -154,7 +219,7 @@ def build_input(self, input_model: 'ResultInput', config: 'JobConfig',
input_file = str_template.substitute()

return {
"commands": ["entos", "-n", str(config.ncores), "dispatch.in"],
"commands": ["entos", "-n", str(config.ncores), "-o", "dispatch.out", "--json-results", "dispatch.in"],
"infiles": {
"dispatch.in": input_file,
"geometry.xyz": xyz_file
Expand Down Expand Up @@ -183,42 +248,88 @@ def write_input_recursive(self, d: Dict[str, Any]) -> List:

def parse_output(self, outfiles: Dict[str, str], input_model: 'ResultInput') -> 'Result':

output_data = {}
dft_map = {
"energy": "scf_total_energy",
"n_iter": "scf_iterations",
}
dft_extras = {
"converged": "scf_converged",
"ao_basis": {
"basis": {"n_functions", "shells"}
},
"density": "scf_density",
"orbitals": "scf_orbitals",
"fock": "fock"
}

energy_command_map = {
"dft": dft_map,
# "xtb": xtb_map,
}

gradient_map = {
"energy": "scf_total_energy",
"gradient": "gradient"}

# Initialize properties dictionary
properties = {}

# Parse the output file, collect properties and gradient
output_lines = outfiles["dispatch.out"].split('\n')
gradients = []
natom = len(input_model.molecule.symbols)
for idx, line in enumerate(output_lines):
fields = line.split()
if fields[:1] == ["energy:"]:
properties["scf_total_energy"] = float(fields[-1])
elif fields[:2] == ["Molecular", "Dipole:"]:
properties["scf_dipole_moment"] = [float(x) for x in fields[2:5]]
elif fields[:3] == ["SCF", "converged", "in"]:
properties["scf_iterations"] = int(fields[3])
elif fields == ["Gradient", "(hartree/bohr):"]:
# Gradient is stored as (dE/dx1,dE/dy1,dE/dz1,dE/dx2,dE/dy2,...)
for i in range(idx + 2, idx + 2 + natom):
grad = output_lines[i].strip('\n').split()[1:]
gradients.extend([float(x) for x in grad])

if input_model.driver == 'gradient':
if len(gradients) == 0:
raise ValueError('Gradient not found.')
else:
output_data["return_result"] = gradients
# Determine the energy_command
energy_command = self.determine_energy_command(input_model.model.method)

# Determine whether to use the energy map or the gradient map
if input_model.driver == "energy":
entos_map = energy_command_map[energy_command]
elif input_model.driver == "gradient":
entos_map = gradient_map
else:
raise NotImplementedError(f'Driver {input_model.driver} not implemented for entos.')

# Replace return_result with final_energy if gradient wasn't called
if "return_result" not in output_data:
# Parse the results.json output from entos
load_results = json.loads(outfiles["results.json"])
entos_results = load_results["json_results"]
for key in entos_map.keys():
if key in entos_results:
properties[entos_map[key]] = entos_results[key]

# Determine the correct return_result
output_data = {}
if input_model.driver == 'energy':
if "scf_total_energy" in properties:
output_data["return_result"] = properties["scf_total_energy"]
else:
raise KeyError("Could not find SCF total energy")
raise KeyError(f"Could not find {input_model.model} total energy")
elif input_model.driver == 'gradient':
if "gradient" in properties:
output_data["return_result"] = properties["gradient"]
properties.pop("gradient")
else:
raise KeyError('Gradient not found.')
else:
raise NotImplementedError(f'Driver {input_model.driver} not implemented for entos.')

output_data["properties"] = properties
output_data['schema_name'] = 'qcschema_output'
output_data['success'] = True

return Result(**{**input_model.dict(), **output_data})

# Determine the energy_command
def determine_energy_command(self, method):
"""
Determine the energy command in entos
"""

if method.upper() in self._dft_functionals:
energy_command = "dft"
# For now entos supports HF calculations through the dft energy_command with xc = HF
elif method.upper() == "HF":
energy_command = "dft"
else:
energy_command = method.lower()

# Check method is supported
if energy_command not in self._energy_commands:
raise InputError(f'Energy method, {method}, not implemented for entos.')

return energy_command
2 changes: 1 addition & 1 deletion qcengine/testing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ def get_job(self):
"terachem": which("terachem", return_bool=True),
"molpro": is_program_new_enough("molpro", "2018.1"),
"mopac": is_program_new_enough("mopac", "2016"),
"entos": is_program_new_enough("entos", "0.5"),
"entos": is_program_new_enough("entos", "0.6"),
"cfour": which('xcfour', return_bool=True),
"gamess": which('rungms', return_bool=True),
"nwchem": which('nwchem', return_bool=True),
Expand Down
2 changes: 2 additions & 0 deletions qcengine/tests/test_standard_suite.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
("psi4", {"method": "hf", "basis": "6-31G"}),
("rdkit", {"method": "UFF"}),
("torchani", {"method": "ANI1x"}),
("entos", {"method": "pbe", "basis": "6-31G"}),
] # yapf: disable


Expand Down Expand Up @@ -59,6 +60,7 @@ def test_compute_gradient(program, model):
("psi4", {"method": "bad"}),
("rdkit", {"method": "bad"}),
("torchani", {"method": "bad"}),
("entos", {"method": "bad"}),
]) # yapf: disable
def test_compute_bad_models(program, model):
if not testing.has_program(program):
Expand Down

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