Interface to GDMA Distributed Multipole Analysis by A. J. Stone — gdma()

Code author: Anthony J. Stone, Andrew C. Simmonett

Section author: Andrew C. Simmonett

Module: Keywords, PSI Variables, GDMA_INTERFACE

Installation

Binary

• 

• GDMA is available as a conda package for Linux and macOS (and Windows, through the Ubuntu shell).

• If using the PSI4 binary, gdma has already been installed alongside.

• If using PSI4 built from source, and anaconda or miniconda has already been installed (instructions at Quick Installation), gdma can be obtained through conda install gdma -c psi4. Then enable it as a feature with ENABLE_gdma, hint its location with CMAKE_PREFIX_PATH, and rebuild PSI4 to detect gdma and activate dependent code.

• To remove a conda installation, conda remove gdma.

Source

• 

• If using PSI4 built from source and you want gdma built from from source also, enable it as a feature with ENABLE_gdma, and let the build system fetch and build it and activate dependent code.

Input

The distributed multipole analysis (DMA) technique, developed by Anthony J. Stone and implemented by him into the GDMA package, is available in PSI4. The current implementation simply embeds Stone’s GDMA code into the main executable, and generates the appropriate input files automatically. The program takes as input a data file, and a Gaussian formatted checkpoint (see Section FCHK) file. The simplest usage of the GDMA code is demonstrated below, along with a listing of the options supported; these options correspond to the options described in the GDMA manual.

If more advanced usage is desired, which is not is permitted by the options listed below, the user may provide their own data file containing keywords to control the GDMA code. Simply place the data file in the directory PSI4 is called from, and provide the file name as the datafile argument to the gdma() routine. For example, if GDMA data file is called control.dma, the GDMA code is called as follows:

grad, wfn = gradient('mp2', return_wfn=True)
gdma(wfn, datafile='control.dma')

An FCHK file will be generated for the GDMA code to read; this file will have the prefix given by WRITER_FILE_LABEL (if set), or else by the name of the output file plus the name of the current molecule, and the suffix will be ‘.fchk’. This FCHK file name should be passed to the ‘File’ keyword in the DGMA data file, to ensure that the GDMA code reads the correct wavefunction information.

After running, two matrices of results can be accessed:

dma_results = get_array_variable('DMA DISTRIBUTED MULTIPOLES')
tot_results = get_array_variable('DMA TOTAL MULTIPOLES')

The first contains distributed multipoles, in units given by GDMA_MULTIPOLE_UNITS, with the row index corresponding to the site and the column index referencing the multipole component. Both indices are zero based, and the \(Q^l_m\) components of the multipoles are ordered as \(Q^0_0, Q^1_0, Q^1_{1c}, Q^1_{1s}, Q^2_0, Q^2_{1c}, Q^2_{1s}, Q^2_{2c}, Q^2_{2s}, \ldots\) The second matrix returned has a single row, whose columns are the total multipoles, translated to GDMA_ORIGIN, and summed.

psi4.gdma(wfn)

Function to use wavefunction information in wfn and, if specified, additional commands in filename to run GDMA analysis with A. J. Stone’s program.

New in version 0.6.

Returns:

None

Parameters:

• wfn (Wavefunction) – set of molecule, basis, orbitals from which to generate DMA analysis

• datafile (str) – optional control file (see GDMA manual) to peform more complicated DMA analyses. If this option is used, the File keyword must be set to read a filename.fchk, where filename is provided by WRITER_FILE_LABEL .

Examples:

>>> # [1] DMA analysis from MP2 wavefunction.  N.B. gradient must be requested to generate MP2 density.
>>> grad, wfn = gradient('mp2', return_wfn=True)
>>> gdma(wfn)

Options

GDMA_LIMIT

The order of multipole expansion on each site. Currently limited to the same order for all sites; for more advanced usage a user-provided GDMA data file should be provided.

• Type: integer

• Default: 2

GDMA_ORIGIN

The origin (in Angstrom, expressed as an [x, y, z] array) about which the total multipoles will be computed during DMA. Useful for determining single site expansions at an arbitrary point.

• Type: array

• Default: No Default

GDMA_MULTIPOLE_UNITS

Whether to print DMA results in atomic units or SI.

• Type: string

• Possible Values: AU

• Default: AU SI

GDMA_RADIUS

The radii to be used, overriding the defaults. Specified as an array [ n1, r1, n2, r2, … ] where n1,n2,n3… are atom type strings and r1,r2,r3 are radii in Angstrom.

• Type: array

• Default: No Default

GDMA_SWITCH

The value to switch between the older standard DMA and the new grid-based approach. Pairs of primitives whose exponents sum is above this value will be treated using standard DMA. Set to 0 to force all pairs to be treated with standard DMA.

• Type: double

• Default: 4.0

How to configure gdma for building Psi4

Role and Dependencies

• Role — In PSI4, GDMA is a library that provides additional quantum chemical capabilities (multipole analysis).

• Downstream Dependencies — PSI4 (\(\Leftarrow\) optional) gdma

• Upstream Dependencies — gdma \(\Leftarrow\) Fortran

CMake Variables

• ENABLE_gdma — CMake variable toggling whether Psi4 builds with gdma

• CMAKE_PREFIX_PATH — CMake list variable to specify where pre-built dependencies can be found. For gdma, set to an installation directory containing include/GDMA/GDMA_MANGLE.h

• gdma_DIR — CMake variable to specify where pre-built gdma can be found. Set to installation directory containing share/cmake/gdma/gdmaConfig.cmake

• CMAKE_DISABLE_FIND_PACKAGE_gdma — CMake variable to force internal build of gdma instead of detecting pre-built

• CMAKE_INSIST_FIND_PACKAGE_gdma — CMake variable to force detecting pre-built gdma and not falling back on internal build

Examples

1. Build bundled

>>> cmake -DENABLE_gdma=ON

2. Build without gdma

>>> cmake

3. Link against pre-built

>>> cmake -DENABLE_gdma=ON -DCMAKE_PREFIX_PATH=/path/to/gdma/root

>>> cmake -DENABLE_gdma=ON -Dgdma_DIR=/path/to/gdma/configdir

4. Build bundled despite pre-built being detectable

>>> cmake -DENABLE_gdma=ON -DCMAKE_PREFIX_PATH=/path/to/unwanted/gdma/root/and/wanted/other/dependencies/root -DCMAKE_DISABLE_FIND_PACKAGE_gdma=ON