ns_T_dependent_analysis

#!/bin/bash

if [ $# -lt 3 ]; then
    echo "Usage: $0 root analysis_commands_file T [ T ... ]" 1>&2
    exit 1
fi

root=$1; shift
analysis_commands_file=$1; shift

traj_root=${root}.traj
newest_traj=`ls -tr ${traj_root}.[0-9]*xyz | tail -1`
traj_combined=${traj_root}.combined_every_100

if [ $newest_traj -nt ${traj_combined}.xyz ]; then
    echo "merging trajectories" 1>&2
    ../../../ns_process_traj -t -i 100 -f xyz -o ${traj_combined}.xyz ${traj_root}.[0-9]*xyz
else
    echo "No need to merge trajectories" 1>&2
fi

if [[ ${traj_combined}.xyz -nt ${traj_combined}.rdfd_1_1.raw || ${traj_combined}.xyz -nt ${traj_combined}.rdfd_1_2.raw ]]; then
    echo "Doing RDF analyses with commands:" 1>&2
    cat $analysis_commands_file 1>&2
    echo ""
    structure_analysis_traj commandfile=$analysis_commands_file infile=${traj_combined}.xyz
else
    echo "No need to recalculate RDF's" 1>&2
fi

echo "Setting weights on analyses" 1>&2
../../../ns_set_analysis_weights -T $* -e ${root}.energies -i 100 -a ${traj_combined}.*.raw  -t ${traj_combined}.xyz

for f in ${traj_combined}.rdfd*.raw.T_*; do
    echo "Doing weighted mean on $f" 1>&2
    mean_var_correl infile=$f outfile=${f/.raw/} mean
done