Ineffiencies in computing the numerical hessian

1) Maybe due to starting LAMMPS 2N times.
2) Maybe due to use of popen.
3) Could be due to heavy file I/O, sice that 's the only way to communicate with LAMMPS ...

Below are some timing results:

Legend:
totalTime - total time take for computing the hessian
timeNeib - time taken to compute the neighbour lists
timePerturb - total time spent inside perturb() per a FULL hessian calculation
timeLAMMPS - total time spent inside the popen() call which runs LAMMPS
fileTime - total time spent doing file I/O for atlking to LAMMPS
timeHess - time spent manipulating the hessian dict structure

totalTime timeNeib timePerturb timeLAMMPS fileTime timeHess
49.7423419952 0.434784173965 48.5797655582 36.8780109882 11.70175457 0.727792263031
63.6533300877 0.439907073975 62.4323446751 50.4112865925 12.0210580826 0.781078338623
70.9052629471 0.468246936798 69.3777544498 55.5753176212 13.8024368286 1.05926156044
72.0013990402 0.472586154938 70.4885210991 55.9716053009 14.5169157982 1.04029178619
75.1916220188 0.476332902908 73.6517179012 59.05403018 14.5976877213 1.06357121468
75.3300080299 0.479758024216 73.775904417 59.0307564735 14.7451479435 1.07434558868
75.5174300671 0.566131830215 73.8336679935 59.0396382809 14.7940297127 1.1176302433
75.4272179604 0.481420993805 73.8312358856 59.0277297497 14.8035061359 1.11456108093
75.4155731201 0.489336013794 73.8398208618 59.0288999081 14.8109209538 1.08641624451
75.5248250961 0.570980072021 73.8176853657 59.0196013451 14.7980840206 1.13615965843