############################################################################## # Code ############################################################################## run_name = 'run9' data_path = '/home/shenglan/MD_simulations/water_box/cubic_2nm_run9' traj = md.load_trr(data_path+'/nvt-pr.trr', top = data_path+'/water-sol.gro') print ('here is some info about the trajectory we are looking at:') print traj ws = WaterStats(traj,run_name) cut_off = 0.5 tic = time.clock() for this_frame in range(ws.n_frames): tic_loop = time.clock() print 'finding tthds for frame %d' % this_frame if str(this_frame) in ws.nearest_tthds: pass else: tthds = ws.make_nearest_nb_tthds(cut_off,this_frame) ws.nearest_tthds.create_dataset(str(this_frame),data = tthds) toc_loop = time.clock() print('Total time for this frame: %.2f' %(toc_loop-tic_loop)) toc = time.clock() print('Total time: %.2f' %(toc-tic)) ws.all_tthds.close() ws.nearest_tthds.close()
############################################################################## # Code ############################################################################## run_name = 'run9' data_path = '/home/shenglan/MD_simulations/water_box/cubic_2nm_run9' traj = md.load_trr(data_path + '/nvt-pr.trr', top=data_path + '/water-sol.gro') print('here is some info about the trajectory we are looking at:') print traj ws = WaterStats(traj, run_name) cut_off = 0.5 tic = time.clock() for this_frame in range(ws.n_frames): tic_loop = time.clock() print 'finding tthds for frame %d' % this_frame if str(this_frame) in ws.nearest_tthds: pass else: tthds = ws.make_nearest_nb_tthds(cut_off, this_frame) ws.nearest_tthds.create_dataset(str(this_frame), data=tthds) toc_loop = time.clock() print('Total time for this frame: %.2f' % (toc_loop - tic_loop)) toc = time.clock() print('Total time: %.2f' % (toc - tic)) ws.all_tthds.close() ws.nearest_tthds.close()