#!/bin/bash
#$ -S /bin/bash
#$ -N jobname
#$ -o output.log

#Script added to database 9/6/05. Author: Michael Seth

# This script was originally for running on Rhodium. Alter the 
# job control stuff above and ROOT below as needed for the
# computer that you are using. 
                                                                                                                   
export ROOT='/My_directory/myjob'

# 
# This runscript is for the purpose of creating a series of 
# restart files that can be used as starting points for 
# a pointwise thermodynamic integration calculation. For this
# type of calculation, what is needed is suitably equilibrated 
# starting points at a suitable range of values of the 
# chosen reaction coordinate. It is assumed that this can be done
# by starting from an equilibrated system at one value and 
# using an slow growth calculation to evolve the value of the reaction
# coordinate. Experience has shown that slow growth is poor for keeping
# equilibration but it is usually good enough to provide 
# "nearly equilibrated" starting points which can be equilibrated for a further short
# time (~1.5 ps) before data aquisition. This does not always work and
# trajectories must be monitored closely to ensure they are
# equilibrated. 

# This script starts from the system equilibrated at one value and runs
# a series of short calculations (1000 timesteps covering 0.25 au distance of coordinate
# which is a bond length in this case). After each calculation the restart file
# is copied and the .prot file saved.
#                                                                                                                  

# First run.
                                                                                                                   
/home/programs/PAW/PAW_20020422/bin/intel/paw_fast.x $ROOT.cntl

# The first value to which the coordinate is stepped to.
                                                                                                                   
old='7.5'                                                                                                             

# The range of values that the coordinate covers in increasing or decreasing
# order from the starting point as appropriate. 

for i in 7.25 7.0 6.75 6.5

# Start of loop
                                                                                                                   
do

# The constraint from the structure file is replaced with the new value.
                                                                                                                   
sed s/VALUE=$old/VALUE=$i/g $ROOT.strc >temp
mv temp $ROOT.strc

# The restart file at the end of the previous calculation is saved.
                                                                                                                   
cp $ROOT.rstrt $ROOT.rstrt.$old

# The .prot file at the end of the previous calculation is saved.

mv $ROOT.prot $ROOT.prot.$old

# Next calculation with the new structure file.
                                                                                                                   
/home/programs/PAW/PAW_20020422/bin/intel/paw_fast.x $ROOT.cntl.1
                                                                                                                   
old=$i

# End of loop
                                                                                                                   
done