Input Writer

iodata/api.py

@@ -30,7 +30,7 @@
 from .utils import LineIterator
 
 
-__all__ = ['load_one', 'load_many', 'dump_one', 'dump_many']
+__all__ = ['load_one', 'load_many', 'dump_one', 'dump_many', 'write_input']
 
 
 def _find_format_modules():
@@ -78,6 +78,42 @@ def _select_format_module(filename: str, attrname: str, fmt: str = None) -> Modu
         attrname, filename))
 
 
+def _find_input_modules():
+    """Return all input modules found with importlib."""
+    result = {}
+    for module_info in iter_modules(import_module('iodata.inputs').__path__):
+        if not module_info.ispkg:
+            format_module = import_module('iodata.inputs.' + module_info.name)
+            result[module_info.name] = format_module
+    return result
+
+
+INPUT_MODULES = _find_input_modules()
+
+
+def _select_input_module(attrname: str, fmt: str) -> ModuleType:
+    """Find an input module with the requested attribute name.
+
+    Parameters
+    ----------
+    attrname
+        The required attribute of the input module.
+    fmt
+        The name of the input module to use.
+
+    Returns
+    -------
+    format_module
+        The module implementing the required input format.
+
+    """
+    if fmt in INPUT_MODULES:
+        if not hasattr(INPUT_MODULES[fmt], attrname):
+            raise ValueError(f'{fmt} input module does not have {attrname}!')
+        return INPUT_MODULES[fmt]
+    raise ValueError(f"Could not find input format {fmt}!")
+
+
 def load_one(filename: str, fmt: str = None, **kwargs) -> IOData:
     """Load data from a file.
 
@@ -188,3 +224,29 @@ def dump_many(iodatas: Iterator[IOData], filename: str, fmt: str = None, **kwarg
     format_module = _select_format_module(filename, 'dump_many', fmt)
     with open(filename, 'w') as f:
         format_module.dump_many(f, iodatas, **kwargs)
+
+
+def write_input(iodata: IOData, filename: str, fmt: str, template: str = None, **kwargs):
+    """Write input file using an instance of IOData for the specified software format.
+
+    Parameters
+    ----------
+    iodatas
+        An IOData instance containing the information needed to write input.
+    filename : str
+        The input file name.
+    fmt : str
+        The name of the software for which input file is generated.
+    template : str, optional
+        The template input file.
+    **kwargs
+        Keyword arguments are passed on to the input-specific write_input function.
+
+    """
+    input_module = _select_input_module('write_input', fmt)
+    # load template as a string
+    if template is not None:
+        with open(template, 'r') as t:
+            template = t.read()
+    with open(filename, 'w') as f:
+        input_module.write_input(f, iodata, template=template, **kwargs)

iodata/inputs/gaussian.py

@@ -0,0 +1,75 @@
+# IODATA is an input and output module for quantum chemistry.
+# Copyright (C) 2011-2019 The IODATA Development Team
+#
+# This file is part of IODATA.
+#
+# IODATA is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# IODATA is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>
+# --
+"""Gaussian Input Module."""
+
+
+# from attr import asdict
+from typing import TextIO
+from string import Template
+
+from ..iodata import IOData
+from ..periodic import num2sym
+from ..utils import angstrom
+
+
+__all__ = []
+
+
+default_template = """\
+#n ${lot}/${obasis_name} ${run_type}
+
+${title}
+
+${charge} ${spinmult}
+${geometry}
+
+"""
+
+
+def write_input(f: TextIO, data: IOData, template: str = None):
+
+    # load IOData dict using attr.asdict because the IOData class uses __slots__
+    # fields = asdict(data)
+    fields = {"atnums": data.atnums,
+              "atcoords": data.atcoords / angstrom,
+              "title": data.title if not None else 'Input Generated by IOData',
+              "run_type": data.run_type if data.run_type is not None else 'energy',
+              # convert spin polarization to multiplicity
+              "spinmult": int(data.spinpol) + 1,
+              "charge": int(data.charge),
+              "lot": data.lot if data.lot is not None else 'hf',
+              "obasis_name": data.obasis_name if data.obasis_name is not None else 'sto-3g',
+              }
+
+    # convert run type to Gaussian keywords
+    run_types = {"energy": "sp", "freq": "freq", "opt": "opt"}
+    fields["run_type"] = run_types[fields["run_type"].lower()]
+
+    # generate geometry (in angstrom)
+    geometry = []
+    for num, coord in zip(fields["atnums"], fields["atcoords"]):
+        geometry.append(f"{num2sym[num]:3} {coord[0]:10.6f} {coord[1]:10.6f} {coord[2]:10.6f}")
+    fields["geometry"] = "\n".join(geometry)
+
+    # get template
+    if template is None:
+        template = default_template
+
+    # populate files & write input
+    print(Template(template).substitute(fields), file=f)

iodata/test/data/template_gaussian.com

@@ -0,0 +1,19 @@
+%chk=gaussian.chk
+%mem=3500MB
+%nprocs=4
+#p ${lot}/${obasis_name} opt scf(tight,xqc,fermi) integral(grid=ultrafine) nosymmetry
+
+${title} ${lot}/${obasis_name} opt-force
+
+0 1
+${geometry}
+
+--Link1--
+%chk=gaussian.chk
+%mem=3500MB
+%nprocs=4
+#p ${lot}/${obasis_name} force guess=read geom=allcheck integral(grid=ultrafine) output=wfn
+
+gaussian.wfn
+
+

iodata/test/test_inputs.py

@@ -0,0 +1,111 @@
+# IODATA is an input and output module for quantum chemistry.
+# Copyright (C) 2011-2019 The IODATA Development Team
+#
+# This file is part of IODATA.
+#
+# IODATA is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# IODATA is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>
+# --
+"""Test iodata.inputs module."""
+
+
+import os
+
+from typing import List
+
+import numpy as np
+
+from ..iodata import IOData
+from ..utils import angstrom
+from ..api import load_one, write_input
+
+try:
+    from importlib_resources import path
+except ImportError:
+    from importlib.resources import path
+
+
+def check_load_input_and_compare(fname: str, expected_lines: List[str]):
+    """Load saved input file and compare to expected input lines.
+
+    Parameters
+    ----------
+    fname : str
+        Input file name to load.
+    expected_lines : sequence of str
+        Expected lines in the input file.
+
+    """
+    with open(fname, 'r') as ifn:
+        content = "".join(ifn.readlines())
+    expected = "\n".join(expected_lines)
+    assert content == expected
+
+
+def test_input_gaussian_from_xyz(tmpdir):
+    # load geometry from xyz file & add level of theory & basis set
+    with path('iodata.test.data', 'water_number.xyz') as fn:
+        mol = load_one(fn)
+    mol.nelec = 10
+    mol.spinpol = 0
+    mol.lot = 'ub3lyp'
+    mol.obasis_name = '6-31g*'
+    # write input in a temporary folder using an input template
+    fname = os.path.join(tmpdir, 'input_from_xyz.com')
+    with path('iodata.test.data', 'template_gaussian.com') as tname:
+        write_input(mol, fname, fmt='gaussian', template=tname)
+    # load input & compare
+    lines = ["%chk=gaussian.chk", "%mem=3500MB", "%nprocs=4",
+             "#p ub3lyp/6-31g* opt scf(tight,xqc,fermi) integral(grid=ultrafine) nosymmetry",
+             "", "Water ub3lyp/6-31g* opt-force", "", "0 1", ""
+             "H     0.783837  -0.492236  -0.000000",
+             "O    -0.000000   0.062020  -0.000000",
+             "H    -0.783837  -0.492236  -0.000000",
+             "", "--Link1--", "%chk=gaussian.chk", "%mem=3500MB", "%nprocs=4",
+             "#p ub3lyp/6-31g* force guess=read geom=allcheck integral(grid=ultrafine) output=wfn",
+             "", "gaussian.wfn", "", "", "", ""]
+    check_load_input_and_compare(fname, lines)
+
+
+def test_input_gaussian_from_iodata(tmpdir):
+
+    # make an instance of IOData for HCl anion
+    data = {"atcoords": np.array([[0.0, 0.0, 0.0], [angstrom, 0.0, 0.0]]),
+            "atnums": np.array([1, 17]), "nelec": 19, "run_type": 'opt',
+            "title": " hydrogen chloride anion", "spinpol": 1}
+    mol = IOData(**data)
+    # write input in a temporary file
+    fname = os.path.join(tmpdir, 'input_from_iodata.com')
+    write_input(mol, fname, fmt='gaussian')
+    # load input & compare
+    expected_lines = ["#n hf/sto-3g opt", "", " hydrogen chloride anion", "", "-1 2",
+                      "H     0.000000   0.000000   0.000000",
+                      "Cl    1.000000   0.000000   0.000000",
+                      "", "", ""]
+    check_load_input_and_compare(fname, expected_lines)
+
+
+def test_input_gaussian_from_fchk(tmpdir):
+    # load fchk
+    with path('iodata.test.data', 'water_hfs_321g.fchk') as fn:
+        mol = load_one(fn)
+    # write input in a temporary file
+    fname = os.path.join(tmpdir, 'input_from_fchk.in')
+    write_input(mol, fname, fmt='gaussian')
+    # compare saved input to expected
+    expected_lines = ["#n rhfs/3-21g sp", "", "water", "", "0 1",
+                      "H     0.000000   0.783837  -0.443405",
+                      "O     0.000000   0.000000   0.110851",
+                      "H    -0.000000  -0.783837  -0.443405",
+                      "", "", ""]
+    check_load_input_and_compare(fname, expected_lines)