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Pedram Tavazohi edited section_Ensemble_Inorder_to_make__.tex
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\section{Ensemble}
Inorder to make an
ensemble, ensemble one has to use two scripts, the "new_randomStructure.py" and a bash script.The new_randomStructure.py creates random initial .bas files and VELOCITIES from the Md runs. while the bash script moves the input files for fireball and the initial files to each directory.
\textbf{The following is the a description one how new_random_Structure works. To make an ensemble we
will only need to use the
final bash script.}
\subsection{new_randomStructure.py}
For new_random_Structure.py to operate, one has to have the following
python script
\begin{minted}{python}
#!/usr/bin/python
import random
import sys
import time
# MODULE DIRECTIONS
# files at the same directory
\begin{itemsize}
\item answer.xyz
\item VELOCITY.dat
\end{itemsize}
Both of these files are generated in the MD part. To use this
module, script one has to type
python randomStructure.py [numTimeSteps in
answer.xyz] [numAtoms in system] [ job number ]
def pull(numAtoms, numTimeSteps, seed,fname,gname):
elements = {'N':'7', 'O':'8', 'H':'1', 'C':'6', 'Au':'79', 'Ag':'47'}
f = open(fname)
b = open('input.bas', 'w')
foo = f.readlines()
for the command line
in foo:
line.rstrip('/n')
same = ranNum(seed,numTimeSteps)
pos = (int(numAtoms)+2) * same + 2
b.write(" "+ str(numAtoms) + '\n') :\\
python new_random_Structure.py \\
For example for
i azobenzene 24 atoms and 60000 MD step we can use :
\begin{minted}{bash}
$ python new_randomStructure.py 60000 24 6
\end{minted}
\subsection{bash script(for bash shell)}
At this point we have to write a bash script which makes directories and copies every file that is needed into the directories and makes soft links to "Fdata" and "fireball.x". Depending one whether we are running on a PC or super computer and the ability of the super computer to do an array job we will use these two methods
\subsubsection{regular bash}
This bash script can be used to run a single job which creates the neccecary directories. \\
First make a directory and call it "MDET",
\begin{minted}{bash}
mkdir MDET
\end{minted}
Let us make a directory that contains "answer.xyz" and "VELOCITY.dat", we can call it "init". Assuming these to files are in
range(0,int(numAtoms)):
temp = foo[pos+i] a directory called MD we will move them to MDET/init
\begin{minted}{bash}
cd MDET
mkdir init
cp ../MD/answer.xyz init/
cp ../MD/answer.xyz init/
\end{minted}
Let us make another directory that contains our input files, we can call it "input". This directory will contain "fireball.in","mdet.input" and "gamma.kpts".\\
We move the new_randomStructure.py to a directory names util.\\
for
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Now We will create a file with name setup.h in
elements:
print elements[key]
temp2=temp.replace(key, elements[key])
temp = temp2
b.write(temp)
g = open(gname)
c = open('VELOCITIES', 'w')
goo = g.readlines()
for line MDET directory using vi or any text editor
\begin{minted}{bash}
$ vi setup.h
\end{minted}
Then we have to copy the following in
goo:
line.rstrip('/n')
pos = (int(numAtoms)+1) * same + 2
c.write(" "+ str(numAtoms) + '\n') the steup.h.
\begin{minted}{bash}
#!/bin/bash
for i in
range(0,int(numAtoms)):
tem = goo[pos+i]
temp3 = tem.split( )
c.write(temp3[4] + " " + temp3[5] + " " + temp3[6] + '\n')
def convert(str):
pass
def ranNum(seed,numTimes):
A = random.randint(1,seed+23)
B = random.randint(1,seed+A)
return (A * int(seed) + B)% numTimes
def main():
print sys.argv
args = sys.argv
numTimeSteps= int(args[1])
numAtoms= args[2]
try:
numJob= args[3]
except:
numJob = random.randint(0,5000)
seed = int(numJob)+ random.randint(0,numTimeSteps)
pull(numAtoms, numTimeSteps, seed, 'answer.xyz','VELOCITY.dat')
main() `seq 1 10`;
do
mkdir ens.$i
cd ens.$i
cp ../init/asnwer.
done
\end{minted}
