gharib85/vhegen

The vibronic Hamiltonian expansion generator for trigonal and tetragonal polyatomic systems.

VHEGEN: A vibronic Hamiltonian expansion generator for trigonal and tetragonal polyatomic systems

VHEGEN (V-ibronic H-amiltonian E-xpansion GEN-erator) is a Python package capable of symbolically generating arbitrarily high order expansion formulas for Jahn-Teller and pseudo-Jahn-Teller vibronic Hamiltonians in vibrational coordinates.

Scope

VHEGEN covers all bimodal Jahn-Teller and pseudo-Jahn-Teller problems in trigonal and tetragonal symmetries, i.e) point groups: C3, C3v, C3h, D3, D3h, D3d, C4, S4, C4v, C4h, D4, D4h, and D2d. Unimodal problems are treated as special cases of their bimodal analogues and hence also covered.

Compatibility

VHEGEN has been tested with Python 2.7 and 3.7 on Linux, macOS, and Windows 10 operating systems.

Dependencies

• Python 2.7/3.7
• SymPy
• NumPy
• a TeX distribution

VHEGEN requires base Python 2 or 3 and external libraries SymPy and NumPy. It is highly recommended the system also has a TeX distribution installed, such as TeX Live. A TeX installation will allow VHEGEN to execute pdflatex on the output .tex file and generate a LaTeX-typeset output .pdf file. If pip is installed, the Python dependencies for VHEGEN can be installed via pip install -r requirements.txt in the main package directory.

Installation

Installation of the VHEGEN package is as simple as uncompressing the package zip to the user's preferred write-allowed directory. This primes the program for procedural use as an executable script, as well as for importing as a package local to the installation directory. To ensure all dependencies are met, one can run python testrun.py in the main directory. This will execute a zeroeth to sixth order expansion of the E"x(e'+e') problem in D3h symmetry. If successful, the execution should terminate after printing "Testrun complete without errors." If a TeX distribution is not set up on the machine, one should remove vhegen_instance.pdflatex() from testrun.py before running.

File structure of VHEGEN

• VHEGEN : The main VHEGEN package directory.
  • constraints : Directory containing constraint lookup files, used by the program to obtain branch formulas for specific vibronic problems.
  • modules : Directory containing Python source code files imported by vhegen.py.
  • outputs : Directory for storing generated output files. Output files are of the type: .log, .tex, .toc, and .pdf.
  • tables : Directory containing the lookup tables required by the program in the form of Python files. Included are lookup tables for symmetry eigenvalues, general form of vibronic matrices, and root expansion formulas.
  • config.cfg : The configuration file read during procedural execution of vhegen.py.
  • requirements.txt : File storing the program's Python requirements, for use with pip.
  • vhegen.py : The main program file. It can either be ran from terminal or imported into a Python script local to the VHEGEN directory.
  • testrun.py : A test script using vhegen.py as a package to produce the 0th-6th order expansions for the E"x(e'+e') problem in D3h symmetry.

Using VHEGEN procedurally

VHEGEN is called procedurally by executing python vhegen.py in the main package directory. The program settings for procedural use are read from the configuration file config.cfg in the same directory, the contents of which are described below.

Configuration

In the configuration file, the user specifies the five parameters: input, pdf_out, log_out, e_coords, and basis.

Parameter	Values
input	static, dynamic
pdf_out	true, false
log_out	true, false
e_coords	pol, cart
basis	complex, real

Parameter input is used to specify either static or dynamic input mode (discussed in the next section). When set to true(false), parameter pdf_out enables(disables) application of the TeX pdflatex command to produce a .pdf output file. The output file contains the input vibronic interaction, the matrix form of the vibronic Hamiltonian, and all explicit matrix element expansions typeset via LaTeX. Thus, pdf_out should only be set to true if a TeX distribution is installed on the system. Parameter log_out similarly enables or disables output of a text file, containing all relevant information used in the expansion process, including the independent matrix elements and their symmetry eigenvalues, and the root expansion formulas along with their constraints. All expansions in Sympy readable syntax can be found in the log file. Parameter e_coords is used to specify the coordinate system used for expressing e-type vibrational modes. When e_coords is set to pol, the expansions will be kept in polar coordinates as they were originally constructed. When e_coords is set to cart, the expansions are converted to cartesian coordinates. Both polar and cartesian coordinate expansions may be included in the final output by setting e_coords=both. The basis parameter defines which basis to use for vibronic Hamiltonians involving E-type electronic states. When set to complex/real, the output vibronic Hamiltonian matrix elements are for the complex/real E component states. Both complex and real representations can be output by setting basis=both.

Input

The procedural input to VHEGEN consists of specifying: point group symmetry; irreps of electronic states; irreps of vibrational modes; order(s) of expansion; and an output filename. There exist two input approaches, namely the "dynamic input" and "static input" modes, selected using the input parameter in config.cfg.

Both modes of input follow the same general rules for input syntax. All input parameters are case-insensitive, except the output filename. Symmetries are specified by their usual point group classification. Electronic states and vibrational modes are specified by standard Mulliken symbols for their irreducible representations. Single primes in Mulliken symbols are denoted by an apostrophe ', and double primes are denoted by two apostrophes '' or a quotation mark ". For pJT problems that involve two states or bimodal problems that involve two vibrational modes, either a plus sign + or a comma , can be used to separate the two specified states or modes. When specifying the orders of expansion, a range of orders can be stated by providing non-negative integers as lower and upper inclusive bounds separated by a comma, e.g., 0,6. If expansion at a single order is desired, then only an integer is keyed in. Output filename should avoid any operating system dependent illegal characters. If the filename parameter is unspecified or left empty, the output filename will default to value output.

Dynamic

When dynamic input mode is specified in the configuration file, the user enters problem parameters and output filename dynamically through terminal prompts after executing python vhegen.py. Any additional arguments made when calling the program will be ignored if set to dynamic input. The user will be re-prompted at each stage if an invalid parameter is entered. The user can receive lists of valid inputs by entering list, and can quit the program by entering exit.

Static

When input mode is set to static, a vibronic problem is specified in-line with the execution of the program via additional arguments. The following additional arguments must be specified in the static input mode: --sym for point group symmetry, --states for electronic state(s), --modes for vibrational mode(s), and --o for order(s) of expansion. Specification of a filename is done by optional argument --f. The general syntax for specifying the additional arguments when executing the program is --arg=value. For example, execution of problem E x (e+a) in C3v symmetry at the third to sixth orders is accomplished in static input mode by python vhegen.py --sym=C3V --states=E --modes=e+a1 --o=3,6.

Output

When called procedurally, outputs generated by VHEGEN are found in subdirectory VHEGEN/outputs. VHEGEN may produce three output files upon completion of a problem:

• .tex file: Always produced. This file contains all final matrix element expansions in the basis, coordinate system, and orders of expansion(s) specified, the matrix form of the vibronic Hamiltonian, and a count of free parameters needed to be fitted. All information is typeset to a compilable LaTeX document.

• .log file: Produced if log_out=true in config.cfg. This is a text file containing auxiliary information regarding the matrix element expansion process, including the independent matrix elements, their symmetry eigenvalues, their root formulas, and the appropriate contraints. It also contains all final matrix element expansions in Sympy syntax.

• .pdf file: Produced if pdf_out=true in config.cfg. This file is a read-friendly version of the .tex output file compiled via pdflatex.

Using VHEGEN as a package

Herein we describe important methods and attributes of the VHEGEN class, made accessible by importing VHEGEN as a package via import vhegen.

Initialization

To initialize an instance of the VHEGEN class, a dictionary containing all vibronic problem parameters for the instance must be specified as its only argument. The input may be prepared by inp.prepare_input, which takes the five parameters: point group symmetry, the electronic state(s), the vibrational mode(s), order(s) of expansion, and an optional filename -- all given as strings following the syntax rules for procedural input. E.g.) initializing an instance of VHEGEN for the (E+A)x(e+a) problem in C4 symmetry at 12th order is shown below.

import vhegen as vhe

params = vhe.inp.prepare_input(sym='C4', states='E+A', modes='e+a', orders='12', filename='output')

vhegen_instance = vhe.VHEGEN(params)

Generating matrix element expansions

Below are the methods which must be sequentially called to generate the full matrix element expansions for a specified vibronic problem. For more details about the methods described, please see Section 5.3 in the associated paper.

Method	Description
set_e_coords(e_coordinate_system)	Defines the coordinate system for problems involving e-type vibrational modes. Allowed arguments for e_coordinate_system are cart, pol, and both.
set_basis(E_component_basis)	Defines the E state component basis for problems involving E-type states. Allowed arguments for E_component_basis are complex, real, and both.
get_eigenvals()	Obtains unique matrix elements and their symmetry eigenvalues by initializing attribute eigenvals.
get_matrix_form()	Obtain matrix product form of the vibronic Hamiltonian, and stores in attribute matrix.
get_formulas()	Performs lookup of root expansion formulas along with the required constraints, storing them in attributes formulas and constraints respectively.
get_expansions()	Generate term-by-term expansions at all specified orders, storing them in a nested dictionary in attribute expansions. If basis is set to both, expansions in the real basis will be stored in attribute real_expansions.

The auto() method

The methods discussed in the previous subsection can be immediately performed after initialization of a VHEGEN instance by the auto() method. This method sequentially calls all mandaory processes discussed above to generate the expansions attribute including all matrix elements. It will also transform to the real E component basis if applicable. Below is an example script of how one would ggenerate the expanded matrix elements for a specific vibronic Hamiltonian at the desired orders.

import vhegen as vhe 

params = vhe.inp.prepare_input(sym=`D4h', states=`Eg+A1u', modes=`eg+b2u', orders=`0,10')

vhegen_instance = vhe.VHEGEN(params)

vhegen_instance.auto()

print(vhegen_instance.expansions)

Expansion output

The final expansions may be viewed by printing attribute expansions. Alternatively they may also be checked by executing method pdflatex(path) to produce a compiled output .pdf file similarly in procedural usage. If path is left unspecified, the output .pdf will be sent to the outputs subdirectory as it is in procedural usage.

Authors

• Robert A. Lang (University of Toronto)
• Riley J. Hickman (University of Toronto)
• Tao Zeng (York University)