CMIstark user guide

This program can calculate, view, and analyze the energy levels of adiabatic Stark energy curves of linear, symmetric top and asymmetric top molecules.

The program package is developed and maintained by the Controlled Molecule Imaging group (CMI) at the Center for Free-Electron Laser Science (CFEL), Hamburg, Germany.

It is documented in

• Yuan-Pin Chang, Frank Filsinger, Boris G. Sartakov, Jochen Küpper, Comp. Phys. Comm., 185, 339 (2014).
• arXiv:1308.4076 [physics] (eprint of the above CPC paper).

See [Chang2014] for the full reference and links.

General usage

The following provides examples of the general usage.

Todo

Yuan-Pin, you misunderstood my earlier todos. You should first write about the general usagem adn then provide a specific example command at the end of the section of each tool. Put together, these shall give a working example. At every stage, you should provide info on the actual output. It will surely be very useful to even provide the output graphics of plot.

Calculate the Stark energies of water:

cmistark_calculate_energy --isomer=0 --Jmax_calc=10 --Jmax_save=2 --water --dc-fields=0:150:16

After the calculation finishes, it yields a Stark energy file water.molecule.

Plot the Stark energy file water.molecule:

cmistark_plot_energy --Jmax=0 water.molecule

A plot of the Stark energy of J=0 state for water will be created.

Print the Stark energy from the file water.molecule:

cmistark_print_energy --Jmax=0 water.molecule

And the print result is:

# state: 0 0 0 0 0
0.0 0.0 0.0
10.0 -26.1645127287 5.23264284222
20.0 -104.652856844 10.4642471557
30.0 -235.449455843 15.6937755522
40.0 -418.528367889 20.9201929214
50.0 -653.853314271 26.1424675625
60.0 -941.377719139 31.3595723071
70.0 -1281.04476041 36.57048563
80.0 -1672.78743174 41.7741927455
90.0 -2116.52861532 46.9696866871
100.0 -2612.18116548 52.1559693657
110.0 -3159.64800264 57.332052607
120.0 -3758.82221762 62.496959162
130.0 -4409.58718588 67.6497236918
140.0 -5111.81669146 72.7893937211
150.0 -5865.3750603 72.7893937211
Closing remaining open files:water.molecule...done

cmistark_calculate_energy

A (command line) script file called cmistark_calculate_energy is provided as a driver for the calculation of Stark curves. Its command-line options are the following:

--help: help
--<moleculename>: specify which molecule is used in the calculation.
--dc-fields=: specify the range of the DC electric field (in kV/cm) by the following way: start:end:step, example: --dc-fields=0:150:151.
--Jmax_calc=: specify the maximum value of J included in the calculation.
--Jmax_save=: specify the maximum value of J of the Stark curves saved in the output file.
--Jmin=:      specify the minimum value of J included in the calculation.
--Mmax=:      specify the maximum value of M included in the calculation. [TM: What is the default?  Jmax_calc?]
--isomer=:    specify which isomer is used, when <moleculename> has more than one isomer defined in moleculeparameter.py

Example of using cmistark_calculate_energy with options:

cmistark_calculate_energy --isomer=0 --Jmax_calc=40 --Jmax_save=20 --3-aminophenol --dc-fields=0:150:151

After executing this command line, the script will use cmistark packages to calculate stark energies of isomer 0 of 3-aminophenol up to J=40, and save results up to J=20 in an output file called 3-aminophenol.molecule. The Stark curve of each quantum state starts from 0 to 150kV/cm with a step of 1kV/cm.

The output file <moleculename>.molecule stores Stark curves of individual quantum states a data format called HDF5. Such a file format can be read directly by using PyTables packages in Python. Two scripts in this program, cmistark_plot_energy and cmistark_print_energy are provided to easily access these <moleculename>.molecule files. Their options and descriptions are provided below.

cmistark_print_energy

The script file called cmistark_print_energy can access existing Stark files (<moleculename>.molecule) and print the stored curves on the screen. Options:

--help: help
--Jmin=, --Jmax=: specify min. or max. value of J
--Kamax=: specify max. value of Ka
--Mmin=, --Mmax=: specify min. or max. value of M
--isomer=: specify which isomer to print

Example of using cmistark_print_energy with options:

cmistark_print_energy --Jmin=0 --Jmax=2 --Mmin=1 --Mmax=1 <moleculename>.molecule

cmistark_plot_energy

The script file called cmistark_plot_energy can access existing Stark files (<moleculename>.molecule) and plot the stored curves. Options:

--help: help
--energy-unit=: specify the unit of energy, options: MHz, invcm, J
--Jmin=, --Jmax=: specify min. or max. value of J
--Mmin=, --Mmax=: specify min. or max. value of M
--Kamax=: specify max. value of Ka
--states=: specify states to plot, format: J K_a K_c or J K_a K_c M, when M is not specified,
           all M levels of the J state are plotted. Example: "000,1010"
--dipole: plot the effective dipole moments
--isomer=: specify which isomer to plot

Example of using cmistark_plot_energy with options:

cmistark_plot_energy --Jmin=0 --Jmax=2 --Mmin=1 --Mmax=1 <moleculename>.molecule