Thursday, March 19, 2015

my understanding about linux/unix and windows

in Linux
there are several shell types.

1. Bourne Shell
PATH : PATH is an environmental variable in Linux and other Unix-like operating systems that tells the shell which directories to search for executable files (i.e., ready-to-run programs) in response to commands issued by a user.
examples:
PATH="/usr/sbin:$PATH"
or
export PATH=$PATH:/usr/sbin

EXPORT
examples:
export PATH=$PATH:/path/to/dir1:/path/to/dir2
 
2. CSH
Example: 
set path = ($path /usr/local/bin /scripts/admin)

3. KSH
4. TCSH
Example:
setenv PATH $PATH:/usr/local/bin:/scripts/admin

.bashrc (.bashrc, .tcshrc, .kshrc) definition: This file is normally read by interactive shells only. Here is the place to define your aliases, functions and other interactive features like your prompt.
.bash_profile and .profile

Classically, .profile is used by Bourne Shell, and is probably supported by Bash as a legacy measure. Again, .login and .cshrc were used by C Shell.

The .bash_profile would be used once, at login. The .bashrc script is read every time a shell is started. This is analogous to .cshrc for C Shell.
One consequence is that stuff in .bashrc should be as lightweight (minimal) as possible to reduce the overhead when starting a non-login shell.



Wednesday, March 18, 2015

Install Cantera in windows 7/8 and linux machines

Some of following content copied from other website.

Windows installation(has done in windows 7 and 8 machines)

1. Download Python from python.org
2. Choose python-2.7.9
3. Install it.
4. Download numpy-1.9.2-win32-superpack-python2.7 from website http://sourceforge.net/projects/numpy/files.
5. Make sure that you select .exe file. Somehow I do not like whl file.
6. Install it and make sure it is installed in the previous python home directory.
7. Download (32bit, not 64bit, somehow I have problems for 64bit versions. The good news is that both windows 7 and 8 are compatible for 32bit versions) Cantera-2.1.2-x86.msi and Cantera-Python-2.1.2-x86-py2.7.msi files.
8. Install it. Make sure you SHOULD install Cantera-Python-2.1.2-x86-py2.7.msi into the previous python home directory.
9. Now open python command line or shell GUI interface. Input following commands.
import cantera
gas = cantera.Solution('gri30.cti')
h2o = cantera.PureFluid('liquidvapor.cti', 'water')
 
If everything is fine and you are lucky, you should successfully install the
cantera in your windows machine.  

Linux/Unix installation: not completed and tested yet
1. go to website: http://sourceforge.net/projects/cantera/
2. download the file cantera-2.1.2.tar.gz
3. tar xzvf  cantera-2.1.2.tar.gz
4. go to website http://sourceforge.net/projects/numpy/
5. download file numpy-1.9.2.tar.gz\
6. tax xzvf  numpy-1.9.2.tar.gz
7. cd numpy-1.9.2
8. python setup.py install --home=$HOME/python_modules
 

The “ignition delay time” can be considered the time at which the reaction “takes off”.  For our purposes, this can be considered the time at which the temperature rise corresponds to approximately 50% of the final value.

Wednesday, January 21, 2015

how to use Gaussian to calculate enthalpy, free energy, and entropy

Q1: What is

CBS-4M
CBS-QB3
CBS-APNO?

They are various Complete Basis Set (CBS) methods of Petersson and coworkers for computing very accurate energies
Q2: how many calculations they include?
It includes geometry optimization and frequency calculations.
It include MP2, MP4, CCSD calculations too.

Q3: why no basis sets are required in the Gaussian input file?
These methods will automatically assign basis sets for atoms.