Commit 3e4d798a authored by Alan O'Cais's avatar Alan O'Cais

Merge branch 'adress-analysis-scripts-tools' into 'master'

Adress analysis scripts tools

See merge request e-cam/E-CAM-Library!69
parents 61c84580 0ed15850
......@@ -314,5 +314,3 @@ When *gmx mdrun* finished normally (with the above mentioned setup), we have sev
The files for the water example can be found here:
:download:`spc-example.tar.gz <spc-example.tar.gz>`
:orphan:
.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
template. Make sure that any time you use ReST syntax (such as for ".. sidebar::" below), it needs to be preceded
and followed by white space (if you see warnings when this file is built they this is a common origin for problems).
.. Firstly, let's add technical info as a sidebar and allow text below to wrap around it. This list is a work in
progress, please help us improve it. We use *definition lists* of ReST_ to make this readable.
.. sidebar:: Software Technical Information
Name
Tools for AdResS.
Language
C/C++, Python, Fortran, BASH, AWK
Licence
Opensource
Application Documentation
See GROMACS web page: `<http://www.gromacs.org>`_. For analysis tools and thermodynamic force calculation see VOTCA web page: `<http://www.votca.org/home>`_. Visualize molecular dynamics with `VMD <http://www.ks.uiuc.edu/Research/vmd/>`_.
Documentation Tool
none
Relevant Training Material
none
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
################
Tools for AdResS
################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
Purpose of Module
_________________
One purpose of our project is to promote GC-AdResS as a method. It is an advanced method, for people with experience, and once the simulation is done there are several properties and checks to consider to make sure that the simulation was successful.
This module provides little tools to make working with AdResS easier.
Content:
1) how to mask the configuration (output from a full atomistic simulation run) to generate the double resolution configuration.
2) Quick and dirty: get the reference coordinate from the GROMACS input file
3) Checks for the density (for both geometries currently implemented in GROMACS version 5.1.5)
4) Check the temperature on the fly
5) A short fortran code to calculate the distribution of the angles in slab-like AdResS simulation.
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_
Quick and fast data grab from the configuration file:
::
tail conf.gro | awk '(NF==3){print $1/2.0,$2/2.0,$3/2.0}'
How to mask the configuration for setting it up for the AdResS simulation. A straigh forward way is using `VOTCA <http://www.votca.org/tutorials>`_ :
::
csg_map --cg mapping_scheme.xml --hybrid --trj input_file.gro --out output_file.gro --top atomistic_run/topol.tpr
Check temperature on the fly from the output md.log:
::
#!/bin/bash
grep -A 1 --no-group-separator Lambda md.log | grep -v Step | awk '{print $1}' > mdlogging1
grep -A 1 --no-group-separator Temp md.log | grep -v Temp | awk '{print $2}' > mdlogging2
paste mdlogging1 mdlogging2
paste mdlogging1 mdlogging2 >temperature
rm mdlogging1 mdlogging2
Quick grab of the density in the xsplit (slab like) configuration. One way is using the tool from `GROMACS <http://www.gromacs.org>`_:
::
gmx density -d X -f trajectory_file.xtc -sl 50
Quick grab of the density in the sphere configuration. We use `VOTCA <http://www.votca.org/tutorials>`_ for it:
::
csg_density -- axis r -- rmax 10. --ref [x_ref,y_ref,z_ref] --trj trajectory_input.xtc --top topol.tpr --out SOL.dens.out
Collect the p(N) data and combine them in one file. For that we use `VMD <http://www.ks.uiuc.edu/Research/vmd/>`_, it includes a script called topotools, which is used to handle the trajectory. This script can be run from the command line directly:
::
vmd -dispdev text -e extract_coord.tcl
grep -B1 "Frame" WCG.xyz > a
sed '/Frame/ {$!N;d;}' a > column2
grep -B0 "Frame" WCG.xyz > a
sed -i s/Frame// a
sed -i s/--// a
sed -i s/:// a
sed '/^$/d' a > column1
paste column1 column2|awk '{print $1, $2}' > dat.3nm.pn.WCG.dat
And the corresponding extract_coord.tcl:
::
package require topotools 1.2
mol new conf.gro
mol addfile traj_comp.xtc type xtc waitfor all first 0 last -1 step 1
topo writevarxyz WCG.xyz selmod "name WCG and (x>285 and x<315)"
exit
All the small scripts are available as files:
:download:`analysis tools source code <./analysis.tools.tar.gz>`
......@@ -11,5 +11,4 @@ The patch for the abrupt AdResS code is:
:download:`Downloadable version of patch file <localT_abrupt_adress.patch>`
.. :language: c,c++
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