QCT Bayesian Statistics
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| - | The following is our reference implementation of the the hard sphere free energy calculation of JCP129(13):134505. | + | The three steps used in our version of QCT ([http://link.aip.org/link/?JCPSA6/129/134505/1 JCP129(13):134505]) are |
| + | # Calculate <DU>_0(lambda) from a solvent-only system | ||
| + | # Calculate <DU>_1(lambda) from a solute-solvent system, and | ||
| + | # Calculate HS,IS(lambda) profiles from (1) and (2), respectively. | ||
| - | == Downloading == | + | Computationally, two major python scripts (''calc_du.py'' and ''HS_est.py'') implement this functionality, and their usage is described below. Several helper scripts also exist and their usage will be described in context. |
| - | [[Media:HS_est.tgz | HS_est.tgz]] | + | == Calculating <DU> Profiles, ''calc_du.py'' == |
| - | In order to use this, you must have python with numpy installed on your system and have access to our own utilities directory, ucgrad. | + | === Calculating <F> Profiles, ''calc_u.py'' === |
| - | You can get ucgrad from [http://forcesolve.sourceforge.net forcesolve] (forcesolve/cg_topol/ucgrad) by downloading or directly using svn: | + | == Calculating HS,IS Profiles, ''HS_est.py'' == |
| - | <pre><nowiki> | + | |
| - | svn export http://forcesolve.svn.sourceforge.net/svnroot/forcesolve/trunk/cg_topol/ucgrad ucgrad | + | |
| - | </nowiki></pre> | + | |
| - | To access it using ''from ucgrad import *'' within python, you have three options: | + | [[Script:HS_est.py | HS_est.py]] takes a single parameter file (listing the location of histogram data and its format) as input. |
| - | * Add it to your python site-packages directory (/usr/lib64/python2.4/site-packages/ on my system). | + | |
| - | * Set the variable PYTHONPATH to wherever you keep ucgrad (e.g. $HOME/src/ucgrad). | + | |
| - | * Make sure it is in the current directory. | + | |
| - | + | ||
| - | I use the first and second ones, having added a symlink in site-packages. | + | |
| - | + | ||
| - | == Use == | + | |
| - | This program works on "histogram" files containing a list of numbers -- representing the count in each bin. A single example case is included and can be run with: | + | |
| - | ./HS_est.py -p HS.par -o out.expot | + | |
| - | + | ||
| - | Compare out.expot with the included HS.expot and spreadsheet. | + | |
Revision as of 15:39, 1 September 2009
The three steps used in our version of QCT (JCP129(13):134505) are
- Calculate <DU>_0(lambda) from a solvent-only system
- Calculate <DU>_1(lambda) from a solute-solvent system, and
- Calculate HS,IS(lambda) profiles from (1) and (2), respectively.
Computationally, two major python scripts (calc_du.py and HS_est.py) implement this functionality, and their usage is described below. Several helper scripts also exist and their usage will be described in context.
Calculating <DU> Profiles, calc_du.py
Calculating <F> Profiles, calc_u.py
Calculating HS,IS Profiles, HS_est.py
HS_est.py takes a single parameter file (listing the location of histogram data and its format) as input.
