header = dcd.get_header()
#header.istart = header.nstep_save * (frame_begin - 1)
#header.istart = header.istart + header.nstep_save * frame_begin
#header.nset = int(frame_num / frame_stride)
#header.nset = int((frame_end-frame_begin)/frame_stride) + 1
#header.nstep = header.nstep_save * (frame_num - 1)
#header.nstep_save = header.nstep_save * frame_stride
# Open DCD and read the header
dcd_out = DcdFile(sys.argv[-1])
dcd_out.open_to_write()
dcd_out.set_header(header)
dcd_out.write_header()
# Open TS and read the header
ts = TsFile(sys.argv[2])
ts.open_to_read()
ts.read_header()
# read and write
#imodel = 0
#i_org = 0
while dcd.has_more_data():
if not ts.has_more_data():
print('Not enough data in .ts file (1)')
sys.exit(2)
tsdata, lines = ts.read_onestep()
# skip step=1
if tsdata[0][ts.head_col.step] == 1:
if __name__ == '__main__':
if len(sys.argv) < 5:
print('Usage: %SCRIPT [input Dir] [name] [final ID] [output DIR]')
print(' ID shoule be from 0 to final ID.')
sys.exit(2)
dir_in = sys.argv[1]
name = sys.argv[2]
id_end = int(sys.argv[3])
dir_out = sys.argv[-1]
out_ts_files = []
out_dcd_files = []
#Prepare output files
for id_rep in range(1, id_end + 1):
ts = TsFile('%s/%s_%04i.ts' % (dir_out, name, id_rep))
ts.open_to_write()
out_ts_files.append(ts)
dcd = DcdFile('%s/%s_%04i.dcd' % (dir_out, name, id_rep))
dcd.open_to_write()
out_dcd_files.append(dcd)
in_ts_files = []
in_dcd_files = []
#Open input files
for id_rep in range(1, id_end + 1):
idx = id_rep - 1
ts = TsFile('%s/%s_%04i.ts' % (dir_in, name, id_rep))
ts.open_to_read()
print('Usage: %SCRIPT [input Dir] [name] [final ID] [output DIR]')
print(' ID shoule be from 0 to final ID.')
sys.exit(2)
dir_in = sys.argv[1]
name = sys.argv[2]
id_end = int(sys.argv[3])
dir_out = sys.argv[-1]
#Open input files
in_ts_files = []
in_dcd_files = []
for id_rep in range(1, id_end + 1):
idx = id_rep - 1
ts = TsFile('%s/%s_%04i.ts' % (dir_in, name, id_rep))
ts.open_to_read()
ts.read_header()
in_ts_files.append(ts)
dcd = DcdFile('%s/%s_%04i.dcd' % (dir_in, name, id_rep))
dcd.open_to_read()
dcd.read_header()
in_dcd_files.append(dcd)
# Loop for output label
for id_lab in range(1, id_end + 1):
#Prepare output files
tsout = TsFile('%s/%s_%04i.ts' % (dir_out, name, id_lab))
tsout.open_to_write()
if __name__ == '__main__':
if len(sys.argv) < 5:
print('Usage: %SCRIPT [input Dir] [name] [final ID] [output DIR]')
print(' ID shoule be from 1 to final ID.')
sys.exit(2)
dir_in = sys.argv[1]
name = sys.argv[2]
id_end = int(sys.argv[3])
dir_out = sys.argv[-1]
#Open input files
in_ts_files = []
in_dcd_files = []
for id_rep in range(1, id_end + 1):
ts = TsFile('%s/%s_%04i.ts' % (dir_in, name, id_rep))
ts.open_to_read()
#ts.read_header() ## Commented out since the header will be read later
in_ts_files.append(ts)
dcd = DcdFile('%s/%s_%04i.dcd' % (dir_in, name, id_rep))
dcd.open_to_read()
#dcd.read_header() ## Commented out since the header will be read later
in_dcd_files.append(dcd)
id_finish = 0
while id_finish < id_end:
id_begin_now = id_finish + 1
id_end_now = id_finish + NUM_OUTFILE_OPEN
if id_end_now > id_end:
import sys
from cafysis.file_io.dcd import DcdFile
from cafysis.file_io.ts import TsFile
if __name__ == '__main__':
if len(sys.argv) < 5:
print('Usage: % SCRIPT [name] [Dir 1] [Dir 2] ([Dir 3] ...) [output dir]')
sys.exit(2)
name = sys.argv[1]
dirs = sys.argv[2:-1]
dir_out = sys.argv[-1]
# Prepare output files
out_ts = TsFile( '%s/%s.ts' % (dir_out, name) )
out_ts.open_to_write()
out_dcd = DcdFile( '%s/%s.dcd' % (dir_out, name) )
out_dcd.open_to_write()
nstep_total_ts = 0
nstep_total_dcd = 0
for (i_dir, d) in enumerate(dirs):
in_ts = TsFile( '%s/%s.ts' % (d, name) )
in_ts.open_to_read()
in_ts.read_header()
in_dcd = DcdFile( '%s/%s.dcd' % (d, name) )
in_dcd.open_to_read()
in_dcd.read_header()
nframe_skip = int(sys.argv[2])
nframe_end = int(sys.argv[3])
E_CUTOFF = float(sys.argv[4])
print("# calculated by ts_calc_cv.py")
print("# Search query: {:s}".format(sys.argv[1]))
print("# nframe_skip: {:d}".format(nframe_skip))
print("# nframe_end: {:d}".format(nframe_end))
print("# E_CUTOFF: {:f}".format(E_CUTOFF))
Ts = []
e_sq = {}
e = {}
n = {}
for tsfile in glob.glob(sys.argv[1]):
ts = TsFile(tsfile)
ts.open_to_read()
ts.read_header()
iframe = 0
while ts.has_more_data():
tsdata, tslines = ts.read_onestep()
iframe += 1
if iframe <= nframe_skip:
continue
if iframe > nframe_end:
break
T = float(tsdata[0][ts.head_col.temp])
etot = float(tsdata[0][ts.head_col.e_tot])