CMIstark documentation¶

CMIstark is a software package and tool for DC Stark effect calculations of molecules in electric fields.

See [Chang2014] for a scientific description of version 1.0 and as a formal, citeable reference.

User documentation¶

Installing CMIstark¶

Prerequisites and obtaining CMIstark¶

Since CMIstark is written in Python, you need to install Python; CMIstark requires Python version 3.5 or higher.

In addition, you need various Python extension packages, these include

cmiext
NumPy
SciPy
Tables
Matplotlib

CMIstark is avaiable on GitHub, please contact Jochen Küpper <jochen.kuepper@cfel.de> for further details.

Installing CMIstark¶

A normal installation is performed by simply running the command:

python setup.py install

However, often you do not have the administrative rights to install in global directories, or simply do not want to overrride a global installtion. In this case, you might want to perform a local installation in your user directory using:

python setup.py install --user

A similar setup can be achieved using:

python setup.py develop --user

which, however, sets up the installation in such a way that changes to your source directory are automatically and immediately visible through the installed version. This avoids repeated re-installs while you are developing code.

Once you are satisfied with your changes you might consider reinstalling using one of the above two options.

Fur further details of develop install, see http://naoko.github.io/your-project-install-pip-setup

Installing CMIstark: in user-specified path¶

Use PYTHONUSERBASE to specify the installation path:

setenv PYTHONUSERBASE $HOME/.local
python setup.py install --user

In the above example of installation (in tcsh shell), the module will be installed in the following path:

$HOME/.local/lib/python/site-packages

and the scripts will be installed in the following path:

$HOME/.local/bin

To import modules and call scripts of such user-specific installation, the following environment declarifications are required:

setenv PATH /opt/local/bin:$HOME/.local/bin:$PATH
setenv PYTHONUSERBASE $HOME/.local

The above example is provided for the tcsh shell. You can also then use site module of python in python command prompt to make sure the environment is properly set up. For example:

>>> import site
>>> site.USER_BASE
'$HOME/.local'

Also type “which name of script file” to find the real path of the script called. It should be in “$HOME/.local/bin”.

For further details, see https://docs.python.org/3/install/index.html#inst-alt-install-user and https://docs.python.org/3/using/cmdline.html#envvar-PYTHONUSERBASE

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 -26.1645127287 5.23264284222
0 -104.652856844 10.4642471557
0 -235.449455843 15.6937755522
0 -418.528367889 20.9201929214
0 -653.853314271 26.1424675625
0 -941.377719139 31.3595723071
0 -1281.04476041 36.57048563
0 -1672.78743174 41.7741927455
0 -2116.52861532 46.9696866871
0 -2612.18116548 52.1559693657
0 -3159.64800264 57.332052607
0 -3758.82221762 62.496959162
0 -4409.58718588 67.6497236918
0 -5111.81669146 72.7893937211
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

Add a new molecule to CMIstark¶

Firstly, in the file called moleculeparameter.py (in the cmistark folder), add all relevant molecular constants/parameters as a function. See the examples provided in this file.

Next, in the script file cmistark_calculate_energy (in the script folder), add an option for calling the above added function for the mew molecule. See the examples provided in this file.

Extending and embedding CMIstark¶

Manually accessing the CMIstark results¶

Todo

here we need a short summary and then the references specified below.

The following example source code of Python shows how to read the curve for the 00000 state from <moleculename>.molecule by using PyTables:

import tables
import numpy
stark_file = "<moleculename>.molecule"
f=tables.openFile(stark_file)
array = f.getNode("/_0/_0/_0/_0/_0/dcstarkenergy")
print numpy.array(array.read())

Developer documentation¶

The full documentation of the source code is available in the following subpages. This includes, for instance, available classes and methods, and their respective parameters and return values.

cmistark package¶

Submodules¶

cmistark.molecule module¶

cmistark.moleculeparameters module¶

cmistark.starkeffect module¶

Module contents¶

CMIstark developer guide¶

Here are a few simple guidelines to please be obeyed when working on CMIdiffract

Document your code!
- Use spinx-compatible docstrings to document all classs, methods, functions, etc.
Write code that is compatible with the latest stable Python 3.x version.
Make use of NumPy as much as possible.

Source code formatting¶

CMIstark uses the 4-spaces standard for indentation of blocks.
Do not use tabs, always expand to spaces.
Try to not extend lines beyond 100 characters
Keep the utf-8 coding directive in the first line
Keep the Emacs local variables section at the end of all files, and try to stick to the directives (manually) when not using Emacs.

Version control (git) details¶

CMIstark uses git (Stash) as a version control system with a central repositories in the DESY-CFEL-CMI stash server.
- CMIstark uses the git-flow branching model
  - the principal development branch is develop
  - all new developments should be done on a feature/ branch and, once ready, be branched into develop
- never touch the branch master – this is to be done by the maintainers.
  - the master branch is only for releases, which for CMIstark are rare and surely only after discussion with me. There should never be any development done on master, nor any release preparations. The latter is done on release/, then the release is put onto master, and possibly necessary fixes are done on hotfix/!
- Do not repeatedly branch feature branches into develop instead merge develop into your feature/ branch.
- General documentation work should always be made on develop (only)!
  - commit such doc-only updates as separate commits!
  - one can then merge these doc-only commits into feature/ branches
- never implement a change twice manually! Implement it on the most appropriate branch, then merge it into whatever branch you want to have it!
make sure the git repo stays clean and one can follow it with our turning crazy!

State labels of stored Stark curves¶

In the output file <moleculename>.molecule, each Stark curve has a state label ($J$, $K_a$, $K_c$, $M$, isomer), which represents the adiabatic quantum number label of the rotational state in the field, as well as the type of isomer. $J$, $K_a$, $K_c$, $M$ are integers, assuming no orbital angular momentum and spin of electrons and nuclear spins involved. For all types of rotors, the value of $J$ is not less than zero.

For asymmetric tops and linear rotors, only states with positive $M$ are stored, as all curves of nonzero $M$ states are doubly degenerate. The values of both $K_a$ and $K_c$ are not less than zero for asymmetric tops, or set to zero for linear rotors. The state lable for linear rotors is thus ($J$, $0$, $0$, $M$, isomer).

For symmetric tops, states having products of $K$ and $M$ equal to $+|KM|$ and $-|KM|$ split in the DC electric field. In the output file states, corresponding to negative $|KM|$ are stored with negative $K$ (and positive $M$); this is really an implementation detail and the sign stored with $K$ in this case is always the sign of the product $KM$. We note that states with $K>0$ and $M<0$ also yield $-|KM|$. Thus, all curves of nonzero $M$ states in the output file are also doubly degenerate. Finally, the state label for prolate tops is ($J$, $K$, $0$, $M$, isomer), and ($J$, $0$, $K$, $M$, isomer) for oblate tops.

Structure of <moleculename>.molecule¶

For each state ($J$, $K_a$, $K_c$, $M$,isomer), the Stark energy as function of DC field strength is stored in the following structures:

/_J/_Ka/_Kc/_M/_isomer/dcfield
/_J/_Ka/_Kc/_M/_isomer/dcstarkenergy

The state label ($J$, $K_a$, $K_c$, $M$, isomer) is manifested as a dictionary strcuture here for storing state-specific information.

The following example source code of Python shows how to read the curve for the 00000 state from <moleculename>.molecule by using PyTables:

import tables
import numpy
stark_file = "<moleculename>.molecule"
f=tables.openFile(stark_file)
array = f.getNode("/_0/_0/_0/_0/_0/dcstarkenergy")
print numpy.array(array.read())

A script cmistark_print_energies, that provides ASCII output for specified conditions and states, is provided in the package for convenience.

Descriptions of source code files¶

Three source code files in cmistark folder provide all functions used to calculate and then write/read Stark curves. The above script files perform the calculations by calling these functions. The basic descriptions of each file in lib folder are as follows:

molecule.py: perform the Stark effect calculation by calling functions from starkeffect.py and store results in an output file
moleculeparameter.py: contain all molecular parameters of individual molecules
starkeffect.py: contain all functions, equations and algorithms required for calculating the Stark effect.

(Only for stand-alone version) The descriptions of the rest of the files in the lib folder are as follows:

codata.py: store most scientific constants
const.py: call required math. and phys. constants from codata.py
convert.py: perform unit conversions
hdf5.py: read/write output files in the format of hdf5 via PyTables
moleculeproperty.py: create a molecule (as an object) from a list of atoms
state.py: create state labels and corresponding id numbers
util.py: provide array operations

ToDo list¶

Todo

here we need a short summary and then the references specified below.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/cmistark/checkouts/stable/doc/extending.rst, line 8.)

Todo

References only give a name and a year (and possibly a town) are not useful… If it’s what it is, say private communication. But try to avoid it.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/cmistark/checkouts/stable/doc/references.rst, line 140.)

Todo

For NIST SPec DB I would only provide references for general http://www.nist.gov/pml/data/msd-di/index.cfm, http://www.nist.gov/pml/data/msd-tri/index.cfm, etc. or maybe even only one entry pointing at http://www.nist.gov/pml/data/molspec.cfm

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/cmistark/checkouts/stable/doc/references.rst, line 143.)

Todo

Please write correct names, e.g., using the appropriate umlauts.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/cmistark/checkouts/stable/doc/references.rst, line 148.)

Todo

journals should be printed in italics, volumes in bold

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/cmistark/checkouts/stable/doc/references.rst, line 150.)

Todo

the output formatting should be much nicer… not sure how to do this, but please check. Maybe we can have a table or something like that?

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/cmistark/checkouts/stable/doc/references.rst, line 152.)

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.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/cmistark/checkouts/stable/doc/user-guide.rst, line 25.)

References¶

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Todo

References only give a name and a year (and possibly a town) are not useful… If it’s what it is, say private communication. But try to avoid it.

Todo

For NIST SPec DB I would only provide references for general http://www.nist.gov/pml/data/msd-di/index.cfm, http://www.nist.gov/pml/data/msd-tri/index.cfm, etc. or maybe even only one entry pointing at http://www.nist.gov/pml/data/molspec.cfm

Todo

Please write correct names, e.g., using the appropriate umlauts.

Todo

journals should be printed in italics, volumes in bold

Todo

the output formatting should be much nicer… not sure how to do this, but please check. Maybe we can have a table or something like that?

Table of Contents

CMIstark documentation¶

User documentation¶

Installing CMIstark¶

Prerequisites and obtaining CMIstark¶

Installing CMIstark¶

Installing CMIstark: in user-specified path¶

CMIstark user guide¶

General usage¶

cmistark_calculate_energy¶

cmistark_print_energy¶

cmistark_plot_energy¶

Add a new molecule to CMIstark¶

Extending and embedding CMIstark¶

Manually accessing the CMIstark results¶

Developer documentation¶

cmistark package¶

Submodules¶

cmistark.molecule module¶

cmistark.moleculeparameters module¶

cmistark.starkeffect module¶

Module contents¶

CMIstark developer guide¶

Source code formatting¶

Version control (git) details¶

State labels of stored Stark curves¶

Structure of <moleculename>.molecule¶

Descriptions of source code files¶

ToDo list¶

References¶

Indices and tables¶