Skip to content

Fix header of asci files generated by read_hdf5 #379

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jeanlucf22 merged 1 commit into from
Nov 4, 2025
Merged

Fix header of asci files generated by read_hdf5 #379

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
36 changes: 19 additions & 17 deletions util/read_hdf5.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -665,13 +665,10 @@ def writeAtomsXYZ(xyz_filename, filename, origin, lattice):


''' MAIN '''
# *argv (sys.argv in Python) - Takes an Arbitrary Number of Paramters
# and Stores Them in a List

# USAGE:
# ssh -l user cab.llnl.gov (If Using Cab System)
# python read_hdf5.py [ -bov ] file.hdf5 datasetName

# The '-bov' option should be used to visulaize data with VisIt
# For a plain asci file with data in one column, no '-bov' option should be used
def main():

''' Variables '''
Expand Down Expand Up @@ -800,25 +797,30 @@ def main():
else:

print('\nWrite data...\n')

ndec = 4
with open(output_data_filename, 'w') as tfile:

tfile.write('\n' + str( origin[0] ) + '\t'
+ str( origin[1] ) + '\t'
+ str( origin[2] ) + '\t'
+ str( origin[0] + lattice[0] ) + '\t'
+ str( origin[1] + lattice[1] ) + '\t'
+ str( origin[2] + lattice[2] )
+ ' // cell corners')

tfile.write(str(dim[0]) + '\t' + str(dim[1]) + '\t'
+ str(dim[2]) + ' // mesh')

tfile.write( str(round(lattice[0],ndec)) + '\t'
+ str(round(lattice[1],ndec)) + '\t'
+ str(round(lattice[2],ndec))
+ ' // domain dimensions [Bohr]\n')
tfile.write( str(round(origin[0],ndec)) + '\t'
+ str(round(origin[1],ndec)) + '\t'
+ str(round(origin[2],ndec))
+ ' // lower left corner [Bohr]\n')
tfile.write( str(dim[0]) + '\t'
+ str(dim[1]) + '\t'
+ str(dim[2]) + ' // mesh')

count=0
for i in range( dim[0] ):
for j in range( dim[1] ):
for k in range( dim[2] ):
row = (i * incx) + (j * incy) + k
tfile.write('\n' + str( data[row] ))
count = count + 1

print("Written {} values.".format(count))

# Release Data and Attributes
del data
Expand Down