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Signed-off-by: Geoff Hutchison <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| # This source file is part of the Avogadro project. | ||
| # This source code is released under the 3-Clause BSD License, (see "LICENSE"). | ||
|
|
||
| import argparse | ||
| import json | ||
| import sys | ||
|
|
||
| try: | ||
| import numpy as np | ||
| from xtb.libxtb import VERBOSITY_MUTED | ||
| from xtb.interface import Calculator, Param | ||
| imported = True | ||
| except ImportError: | ||
| imported = False | ||
|
|
||
| def getMetaData(): | ||
| # before we return metadata, make sure xtb is in the path | ||
| if not imported: | ||
| return {} # Avogadro will ignore us now | ||
|
|
||
| metaData = { | ||
| "name": "GFN1", | ||
| "identifier": "GFN1", | ||
| "description": "Calculate GFN1-xtb energies and gradients", | ||
| "inputFormat": "cjson", | ||
| "elements": "1-86", | ||
| "unitCell": False, | ||
| "gradients": True, | ||
| "ion": True, | ||
| "radical": True, | ||
| } | ||
| return metaData | ||
|
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||
|
|
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| def run(filename): | ||
| # we get the molecule from the supplied filename | ||
| # in cjson format (it's a temporary file created by Avogadro) | ||
| with open(filename, "r") as f: | ||
| mol_cjson = json.load(f) | ||
|
|
||
| # first setup the calculator | ||
| atoms = np.array(mol_cjson["atoms"]["elements"]["number"]) | ||
| coord_list = mol_cjson["atoms"]["coords"]["3d"] | ||
| coordinates = np.array(coord_list, dtype=float).reshape(-1, 3) | ||
| # .. we need to convert from Angstrom to Bohr | ||
| coordinates /= 0.52917721067 | ||
|
|
||
| # check for total charge | ||
| # and spin multiplicity | ||
| charge = None # neutral | ||
| spin = None # singlet | ||
| if "properties" in mol_cjson: | ||
| if "totalCharge" in mol_cjson["properties"]: | ||
| charge = mol_cjson["properties"]["totalCharge"] | ||
| if "totalSpinMultiplicity" in mol_cjson["properties"]: | ||
| spin = mol_cjson["properties"]["totalSpinMultiplicity"] | ||
|
|
||
| calc = Calculator(Param.GFN1xTB, atoms, coordinates, | ||
| charge=charge, uhf=spin) | ||
| calc.set_verbosity(VERBOSITY_MUTED) | ||
| res = calc.singlepoint() | ||
|
|
||
| # we loop forever - Avogadro will kill the process when done | ||
| while(True): | ||
| # first print the energy of these coordinates | ||
| print(res.get_energy()) # in Hartree | ||
|
|
||
| # now print the gradient | ||
| # .. we don't want the "[]" in the output | ||
| output = np.array2string(res.get_gradient()) | ||
| output = output.replace("[", "").replace("]", "") | ||
| print(output) | ||
|
|
||
| # read new coordinates from stdin | ||
| for i in range(len(atoms)): | ||
| coordinates[i] = np.fromstring(input(), sep=" ") | ||
| # .. convert from Angstrom to Bohr | ||
| coordinates /= 0.52917721067 | ||
|
|
||
| # update the calculator and run a new calculation | ||
| calc.update(coordinates) | ||
| calc.singlepoint(res) | ||
|
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||
|
|
||
| if __name__ == "__main__": | ||
| parser = argparse.ArgumentParser("GFN1 calculator") | ||
| parser.add_argument("--display-name", action="store_true") | ||
| parser.add_argument("--metadata", action="store_true") | ||
| parser.add_argument("-f", "--file", nargs=1) | ||
| parser.add_argument("--lang", nargs="?", default="en") | ||
| args = vars(parser.parse_args()) | ||
|
|
||
| if args["metadata"]: | ||
| print(json.dumps(getMetaData())) | ||
| elif args["display_name"]: | ||
| name = getMetaData().get("name") | ||
| if name: | ||
| print(name) | ||
| else: | ||
| sys.exit("xtb-python is unavailable") | ||
| elif args["file"]: | ||
| run(args["file"][0]) |
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