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 +78,40 @@ 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(fmt: str) -> ModuleType:
+    """Find an input module with the requested attribute name.
+
+    Parameters
+    ----------
+    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], 'write_input'):
+            raise ValueError(f'{fmt} input module does not have write_input!')
+        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 +222,29 @@ 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
+    ----------
+    iodata
+        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(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 +1,76 @@
+# 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."""
+
+
+import attr
+
+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):
+    """Do not edit this docstring. It will be overwritten."""
+    # load IOData dict using attr.asdict because the IOData class uses __slots__
+    fields = attr.asdict(data, recurse=False)
+
+    fields["atcoords"] = data.atcoords / angstrom
+    # set defaults
+    fields["title"] = data.title if data.title is not None else 'Input Generated by IOData'
+    fields["run_type"] = data.run_type if data.run_type is not None else 'energy'
+    fields["lot"] = data.lot if data.lot is not None else 'hf'
+    fields["obasis_name"] = data.obasis_name if data.obasis_name is not None else 'sto-3g'
+    # convert spin polarization to multiplicity
+    fields["spinmult"] = int(data.spinpol) + 1 if data.spinpol is not None else 1
+    fields["charge"] = int(data.charge) if data.charge is not None else 0
+
+    # 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/inputs/orca.py

@@ -0,0 +1,76 @@
+# 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/>
+# --
+"""Orca Input Module."""
+
+from typing import TextIO
+from string import Template
+from attr import asdict
+
+from ..iodata import IOData
+from ..periodic import num2sym
+from ..utils import angstrom
+
+__all__ = []
+
+
+default_template = """\
+! ${lot} ${obasis_name} ${run_type}
+# ${title}
+*xyz ${charge} ${spinmult}
+${geometry}
+*"""
+
+
+def write_input(f: TextIO, data: IOData, template: str = None):
+    """Do not edit this docstring. It will be overwritten."""
+    # load IOData dict using attr.asdict because the IOData class uses __slots__
+    fields = asdict(data, recurse=False)
+
+    # store atomic coordinates in angstrom
+    fields["atcoords"] = data.atcoords / angstrom
+
+    # replace None for default values
+    fields["title"] = data.title if data.title is not None else 'Input Generated by IOData'
+    fields["run_type"] = data.run_type if data.run_type is not None else 'energy'
+    # convert spin polarization to multiplicity
+    fields["spinmult"] = int(data.spinpol) + 1 if data.spinpol is not None else 1
+    fields["charge"] = int(data.charge) if data.nelec is not None else 0
+    fields["lot"] = data.lot if data.lot is not None else 'HF'
+    fields["obasis_name"] = data.obasis_name if data.obasis_name is not None else 'STO-3G'
+
+    # convert run type to orca keywords
+    run_types = {"energy": "Energy", "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"]):
+        sym = f"{num2sym[num]:3}"
+        # check if template has a %coords block
+        if template is not None and "%coords" in template:
+            sym = f"{sym:>11}"  # adding an appropiate indentation
+        geometry.append(f"{sym} {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/input_gaussian_h2o_opt_ub3lyp.txt

@@ -0,0 +1,22 @@
+%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
+
+
+

iodata/test/data/input_gaussian_hcl_anion_opt_hf.txt

@@ -0,0 +1,9 @@
+#n hf/sto-3g opt
+
+Input Generated by IOData
+
+-1 2
+H     0.000000   0.000000   0.000000
+Cl    1.000000   0.000000   0.000000
+
+

iodata/test/data/input_gaussian_hcl_sp_rhf.txt

@@ -0,0 +1,10 @@
+#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
+
+

iodata/test/data/input_orca_h2o_sp_b3lyp.txt

@@ -0,0 +1,16 @@
+! B3LYP def2-SVP Grid4 TightSCF NOFINALGRID KeepDens
+# Water
+%output PrintLevel Mini Print[ P_Mulliken ] 1 Print[P_AtCharges_M] 1 end
+%pal nprocs 4 end
+%coords
+    CTyp xyz
+    Charge 0
+    Mult 1
+    Units Angs
+    coords
+        H     0.783837  -0.492236  -0.000000
+        O    -0.000000   0.062020  -0.000000
+        H    -0.783837  -0.492236  -0.000000
+    end
+end
+

iodata/test/data/input_orca_hcl_anion_opt_hf.txt

@@ -0,0 +1,6 @@
+! HF STO-3G Opt
+# Input Generated by IOData
+*xyz -1 2
+H     0.000000   0.000000   0.000000
+Cl    1.000000   0.000000   0.000000
+*

iodata/test/data/input_orca_nh3_sp_hf.txt

@@ -0,0 +1,8 @@
+! HF STO-3G Energy
+# Molden file created by orca_2mkl for BaseName=test
+*xyz 0 1
+N    -0.007455   0.044763   0.054913
+H     0.791232   0.011334   0.023580
+H    -0.313244  -0.879581   0.283126
+H    -0.374402   0.246289  -1.069692
+*

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/data/template_orca.com

@@ -0,0 +1,13 @@
+! ${lot} ${obasis_name} Grid4 TightSCF NOFINALGRID KeepDens
+# ${title}
+%output PrintLevel Mini Print[ P_Mulliken ] 1 Print[P_AtCharges_M] 1 end
+%pal nprocs 4 end
+%coords
+    CTyp xyz
+    Charge ${charge}
+    Mult ${spinmult}
+    Units Angs
+    coords
+${geometry}
+    end
+end