This script is used to generate a movie of the time evolution of an energy surface from a WESTPA simulation.

generate_surface_evolution.sh

#!/bin/bash
# Written 29 May 2015 by Alex DeGrave <ajd98@pitt.edu>
# This script generates a movie of a free energy surface, evolving in time.
# The script uses a moving block of width $BLOCK_SIZE.
# A movie is output to evolution_plots/energy_surface_evolution.avi.
# Make sure the utility mencoder is installed. 


############ USER VARIABLES ############
# Set location of westpa tools
WEST_ROOT=~/apps/westpa/
# Set location of west.h5
WESTH5=../west.h5
# Set iteration ranges.
MAX_ITER=1000
FIRST_ITER=1
BLOCK_SIZE=100
STEP_ITER=1
# Set axis labels
X_AXIS_LABEL="Dimension 0"
Y_AXIS_LABEL="Dimension 1"
# Set the bounds for the plot axes.
X_AXIS_LOWER_BOUND=0 
X_AXIS_UPPER_BOUND=30
Y_AXIS_LOWER_BOUND=0
Y_AXIS_UPPER_BOUND=30
#######################################

echo \
"def add_movie_labels(hist,midpoints,binbounds):
    import matplotlib.pyplot as plt
    import h5py

    iterations_reference_file = open('iters.out')
    first_iter = int(iterations_reference_file.readline())
    last_iter  = int(iterations_reference_file.readline())
    iterations_reference_file.close()

    plt.xlabel('$X_AXIS_LABEL')
    plt.ylabel('$Y_AXIS_LABEL')
    plt.title('Iterations %d to %d'%(first_iter,last_iter))

    ca = plt.gca()
    ca.set_xlim([$X_AXIS_LOWER_BOUND,$X_AXIS_UPPER_BOUND])
    ca.set_ylim([$Y_AXIS_LOWER_BOUND,$Y_AXIS_UPPER_BOUND]) 
    return" > surface_plot_functions.py 

mkdir evolution_plots
echo "Running w_pdist..."
$WEST_ROOT/bin/w_pdist -W $WESTH5 --first-iter $FIRST_ITER --last-iter $MAX_ITER  -o pdist_for_surface_evolution.h5 

FIRST_ITER=1
LAST_ITER=$[$FIRST_ITER+$BLOCK_SIZE]

echo "Generating plots..."
while [ $LAST_ITER -le $MAX_ITER ] 
    do echo "working on iteration $LAST_ITER"
    printf -v FIRST_ITER_FORMAT "%05d" $FIRST_ITER 
    printf -v LAST_ITER_FORMAT "%05d" $LAST_ITER
    echo $FIRST_ITER > iters.out
    echo $LAST_ITER >> iters.out
    $WEST_ROOT/bin/plothist average \
        --first-iter $FIRST_ITER --last-iter $LAST_ITER \
        --postprocess-function surface_plot_functions.add_movie_labels \
        --range 0,20 \
        -o evolution_plots/$(echo $FIRST_ITER_FORMAT)_to_$(echo $LAST_ITER_FORMAT).png \
        pdist_for_surface_evolution.h5 0 1 
    FIRST_ITER=$[$FIRST_ITER+$STEP_ITER]
    LAST_ITER=$[$LAST_ITER+$STEP_ITER]
done

cd evolution_plots
mencoder mf://*.png -mf w=800:h=600:fps=25:type=png -ovc lavc -lavcopts vcodec=mpeg4:mbd=2:trell -oac copy -o energy_surface_evolution.avi