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 --: 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 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 ``.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 ``.molecule`` files. Their options and descriptions are provided below. cmistark_print_energy --------------------- The script file called ``cmistark_print_energy`` can access existing Stark files (``.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 .molecule cmistark_plot_energy -------------------- The script file called ``cmistark_plot_energy`` can access existing Stark files (``.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 .molecule .. comment Local Variables: coding: utf-8 fill-column: 80 End: