NWChem

NWChem is a computational chemistry code based on gaussian basis functions or plane-waves.

Setup

You first need to install a working copy of NWChem for ASE to call; follow the instructions on the NWChem website.

The default command that ASE will use to start NWChem is nwchem PREFIX.nwi > PREFIX.nwo. You can change this command by setting the environment variable ASE_NWCHEM_COMMAND. (For example, add a line to your .bashrc with export ASE_NWCHEM_COMMAND="my new command".)

The default command will only allow you to run NWChem on a single core. To run on multiple processors you will need to specify your MPI (or similar) command, which typically requires telling the MPI command the number of tasks to dedicate to the process. An example command to allow multiprocessing is mpirun -n $SLURM_NTASKS nwchem PREFIX.nwi > PREFIX.nwo, for the SLURM queueing system. If you use a different queueing system replace $SLURM_NTASKS with the appropriate variable, such as $PBS_NP.

Examples

Here is a command line example of how to optimize the geometry of a water molecule using the PBE density functional:

$ ase build H2O | ase run nwchem -p xc=PBE -f 0.02
Running: H2O
LBFGS:   0  09:58:54    -2064.914841       1.9673
LBFGS:   1  09:58:55    -2064.976691       0.1723
LBFGS:   2  09:58:55    -2064.977120       0.0642
LBFGS:   3  09:58:55    -2064.977363       0.0495
LBFGS:   4  09:58:56    -2064.977446       0.0233
LBFGS:   5  09:58:56    -2064.977460       0.0059
$ ase gui H2O.traj@-1 -tg "a(1,0,2),d(0,1)"
102.591620591 1.00793234388

An example of creating an NWChem calculator in the python interface is:

from ase.calculators.nwchem import NWChem

calc = NWChem(label='calc/nwchem',
              dft=dict(maxiter=2000,
                       xc='B3LYP'),
              basis='6-31+G*')

Parameters

The NWChem calculator represents nested keyword blocks in the input file using nested Python dictionaries. For example, consider the following block of input:

memory 1024 mb

dft
  xc B3LYP
  mult 2
  odft
  convergence energy 1e-5 density 1e-4 gradient 5e-3
end

This would be represented by the following keyword arguments to the NWChem calculator:

NWChem(memory='1024 mb',
       dft=dict(xc='B3LYP',
                mult=2,
                odft=None,
                convergence=dict(energy=1e-5,
                                 density=1e-4,
                                 gradient=5e-3),
                ),
       )

Most input files can be constructed in this way. The NWChem calculator also has several special keywords which do not directly enter into the input file; these are described in the table below

keyword	type	default value	description
`label`	`str`	`'nwchem'`	Used to name input and output files. Also, used as the default name of the perm and scratch directory, unless otherwise specified.
`theory`	`str`	See description	Theory specifies the kind of calculation you want to do. Currently supported values are `dft`, `scf`, `mp2`, `ccsd`, `tce`, `tddft`, `pspw`, `band`, and `paw`. Other settings may work, but have not been tested. If not provided, the Calculator will attempt to guess based on the provided keywords.
`center`	`bool`	`False`	Whether NWChem should automatically center your atoms. You probably don’t want to change this.
`autosym`	`bool`	`False`	Whether NWChem should automatically symmetrize your atoms. You probably don’t want to change this.
`autoz`	`bool`	`False`	Whether NWChem should automatically generate a Z-matrix for your system.
`basis`	`str`	`3-21G`	If provided with a string, the specified basis set will be used for all atoms. Alternatively, you can set element-specific basis sets by passing a dict, e.g. `basis=dict(C='6-31G', O='3-21G')`.
`basispar`	`str`	`''`	Additional keywords to go in the first line of the `basis` block.
`task`	`str`	See description	What kind of calculation is to be performed, e.g. `'energy'`, `'gradient'`, or `'optimize'`. If not provided, it will be automatically determined by the Calculator.
`symmetry`	`str`	`''`	The symmetry group or number of your system.
`geompar`	`str`	`''`	Additional keywords to go in the first line of the `geometry` block.
`set`	`dict`	`dict()`	A set of keys and values to be added directly to the NWChem rtdb. This isn’t necessary for most commonly done tasks, but it is required for certain functionality in plane-wave mode.
`restart_kw`	`str`	`'start'`	If set to `'restart'`, then the calculation will attempt to restart from whatever restart files are available as specified in the .db file (may need to be combined with other keywords).

class ase.calculators.nwchem.NWChem(restart=None, ignore_bad_restart_file=<object object>, label='nwchem', atoms=None, command=None, **kwargs)[source]

NWChem keywords are specified using (potentially nested) dictionaries. Consider the following input file block:

dft
    odft
    mult 2
    convergence energy 1e-9 density 1e-7 gradient 5e-6
end

This can be generated by the NWChem calculator by using the following settings: >>> from ase.calculators.nwchem import NWChem >>> calc = NWChem(dft={‘odft’: None, … ‘mult’: 2, … ‘convergence’: {‘energy’: 1e-9, … ‘density’: 1e-7, … ‘gradient’: 5e-6, … }, … }, … )

In addition, the calculator supports several special keywords:

theory: str

Which NWChem module should be used to calculate the energies and forces. Supported values are 'dft', 'scf', 'mp2', 'ccsd', 'tce', 'tddft', 'pspw', 'band', and 'paw'. If not provided, the calculator will attempt to guess which theory to use based on the keywords provided by the user.

xc: str

The exchange-correlation functional to use. Only relevant for DFT calculations.

task: str

What type of calculation is to be performed, e.g. 'energy', 'gradient', 'optimize', etc. When using 'SocketIOCalculator', task should be set to 'optimize'. In most other circumstances, task should not be set manually.

basis: str or dict

Which basis set to use for gaussian-type orbital calculations. Set to a string to use the same basis for all elements. To use a different basis for different elements, provide a dict of the form:

>>> calc = NWChem(...,
...               basis={'O': '3-21G',
...                      'Si': '6-31g'})

basispar: str

Additional keywords to put in the NWChem basis block, e.g. 'rel' for relativistic bases.

symmetry: int or str

The point group (for gaussian-type orbital calculations) or space group (for plane-wave calculations) of the system. Supports both group names (e.g. 'c2v', 'Fm3m') and numbers (e.g. 225).

autosym: bool

Whether NWChem should automatically determine the symmetry of the structure (defaults to False).

center: bool

Whether NWChem should automatically center the structure (defaults to False). Enable at your own risk.

autoz: bool

Whether NWChem should automatically construct a Z-matrix for your molecular system (defaults to False).

geompar: str

Additional keywords to put in the NWChem $geometry$ block, e.g. 'nucleus finite' for gaussian-shaped nuclear charges. Do not set 'autosym', 'center', or 'autoz' in this way; instead, use the appropriate keyword described above for these settings.

set: dict

Used to manually create or modify entries in the NWChem rtdb. For example, the following settings enable pseudopotential filtering for plane-wave calculations:

set nwpw:kbpp_ray .true.
set nwpw:kbpp_filter .true.

These settings are generated by the NWChem calculator by passing the arguments:

>>> calc = NWChem(...,
>>>               set={'nwpw:kbpp_ray': True,
>>>                    'nwpw:kbpp_filter': True})

kpts: (int, int, int), or dict

Indicates which k-point mesh to use. Supported syntax is similar to that of GPAW. Implies theory='band'.

bandpath: BandPath object

The band path to use for a band structure calculation. Implies theory='band'.

pretasks: list of dict

Tasks used to produce a better initial guess for the wavefunction. These task typically use a cheaper level of theory or smaller basis set (but not both). The output energy and forces should remain unchanged regardless of the number of tasks or their parameters, but the runtime may be significantly improved.

For example, a MP2 calculation preceded by guesses at the DFT and HF levels would be

>>> calc = NWChem(theory='mp2', basis='aug-cc-pvdz',
>>>               pretasks=[
>>>                   {'dft': {'xc': 'hfexch'},
>>>                    'set': {'lindep:n_dep': 0}},
>>>                   {'theory': 'scf', 'set': {'lindep:n_dep': 0}},
>>>               ])

Each dictionary could contain any of the other parameters, except those which pertain to global configurations (e.g., geometry details, scratch dir).

The default basis set is that of the final step in the calculation, or that of the previous step that which defines a basis set. For example, all steps in the example will use aug-cc-pvdz because the last step is the only one which defines a basis.

Steps which change basis set must use the same theory. The following specification would perform SCF using the 3-21G basis set first, then B3LYP//3-21g, and then B3LYP//6-31G(2df,p)

>>> calc = NWChem(theory='dft', xc='b3lyp', basis='6-31g(2df,p)',
>>>               pretasks=[
>>>                   {'theory': 'scf', 'basis': '3-21g',
>>>                    'set': {'lindep:n_dep': 0}},
>>>                   {'dft': {'xc': 'b3lyp'}},
>>>               ])

The 'set': {'lindep:n_dep': 0} option is highly suggested as a way to avoid errors relating to symmetry changes between tasks.

The calculator will configure appropriate options for saving and loading intermediate wavefunctions, and place an “ignore” task directive between each step so that convergence errors in intermediate steps do not halt execution.