QCT Bayesian Statistics
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| 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. | 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. | ||
| + | |||
| + | == Getting ucgrad Working == | ||
| + | |||
| + | First, in order to use most of these scripts, you must have python with numpy installed on your system and have access to our own utilities directory, ucgrad. | ||
| + | |||
| + | You can get ucgrad from [http://forcesolve.sourceforge.net forcesolve] (forcesolve/cg_topol/ucgrad) by downloading or directly using svn: | ||
| + | <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: | ||
| + | * 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. | ||
| == Calculating <DU> Profiles, ''calc_du.py'' == | == Calculating <DU> Profiles, ''calc_du.py'' == | ||
| + | [[Scripts:calc_du.py]] takes a single parameter file (listing the location of histogram data and its format) as input. | ||
| === Calculating <F> Profiles, ''calc_u.py'' === | === Calculating <F> Profiles, ''calc_u.py'' === | ||
| + | [[Scripts:calc_u.py]] takes a single parameter file (listing the location of histogram data and its format) as input. | ||
| == Calculating HS,IS Profiles, ''HS_est.py'' == | == Calculating HS,IS Profiles, ''HS_est.py'' == | ||
| - | [[Script:HS_est.py | HS_est.py]] takes a single parameter file (listing the location of histogram data and its format) as input. | + | [[Scripts:HS_est.py]] takes a single parameter file (listing the location of histogram data and its format) as input. |
Revision as of 16:15, 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.
Contents |
Getting ucgrad Working
First, in order to use most of these scripts, you must have python with numpy installed on your system and have access to our own utilities directory, ucgrad.
You can get ucgrad from forcesolve (forcesolve/cg_topol/ucgrad) by downloading or directly using svn:
svn export http://forcesolve.svn.sourceforge.net/svnroot/forcesolve/trunk/cg_topol/ucgrad ucgrad
To access it using from ucgrad import * within python, you have three options:
- 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.
Calculating <DU> Profiles, calc_du.py
Scripts:calc_du.py takes a single parameter file (listing the location of histogram data and its format) as input.
Calculating <F> Profiles, calc_u.py
Scripts:calc_u.py takes a single parameter file (listing the location of histogram data and its format) as input.
Calculating HS,IS Profiles, HS_est.py
Scripts:HS_est.py takes a single parameter file (listing the location of histogram data and its format) as input.
