ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

more python 3 compatibility

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-02-23 12:30:03 -05:00
parent 5594868ef2
commit 2d7375798f
8 changed files with 69 additions and 67 deletions
Download Patch File Download Diff File Expand all files Collapse all files

94
tools/python/pizza/cfg.py
View File

@ -6,6 +6,8 @@
# certain rights in this software. This software is distributed under
# the GNU General Public License.
from __future__ import print_function
# cfg tool
oneline = "Convert LAMMPS snapshots to AtomEye CFG format"
@ -65,33 +67,33 @@ class cfg:
ylen = box[4]-box[1]
zlen = box[5]-box[2]
print >>f,"Number of particles = %d " % len(atoms)
print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
print >>f,"H0(1,1) = %20.10f A " % xlen
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(2,2) = %20.10f A " % ylen
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(3,3) = %20.10f A " % zlen
print >>f,"#"
print("Number of particles = %d " % len(atoms), file=f)
print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
print("H0(1,1) = %20.10f A " % xlen, file=f)
print("H0(1,2) = 0.0 A ", file=f)
print("H0(1,3) = 0.0 A ", file=f)
print("H0(2,1) = 0.0 A ", file=f)
print("H0(2,2) = %20.10f A " % ylen, file=f)
print("H0(2,3) = 0.0 A ", file=f)
print("H0(3,1) = 0.0 A ", file=f)
print("H0(3,2) = 0.0 A ", file=f)
print("H0(3,3) = %20.10f A " % zlen, file=f)
print("#", file=f)
for atom in atoms:
itype = int(atom[1])
xfrac = (atom[2]-box[0])/xlen
yfrac = (atom[3]-box[1])/ylen
zfrac = (atom[4]-box[2])/zlen
# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
# print("1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]), file=f)
print("1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
print time,
print(time)
sys.stdout.flush()
n += 1
f.close()
print "\nwrote %d snapshots to %s in CFG format" % (n,file)
print("\nwrote %d snapshots to %s in CFG format" % (n,file))
# --------------------------------------------------------------------
@ -120,33 +122,33 @@ class cfg:
ylen = box[4]-box[1]
zlen = box[5]-box[2]
print >>f,"Number of particles = %d " % len(atoms)
print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
print >>f,"H0(1,1) = %20.10f A " % xlen
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(2,2) = %20.10f A " % ylen
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(3,3) = %20.10f A " % zlen
print >>f,"#"
print("Number of particles = %d " % len(atoms), file=f)
print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
print("H0(1,1) = %20.10f A " % xlen, file=f)
print("H0(1,2) = 0.0 A ", file=f)
print("H0(1,3) = 0.0 A ", file=f)
print("H0(2,1) = 0.0 A ", file=f)
print("H0(2,2) = %20.10f A " % ylen, file=f)
print("H0(2,3) = 0.0 A ", file=f)
print("H0(3,1) = 0.0 A ", file=f)
print("H0(3,2) = 0.0 A ", file=f)
print("H0(3,3) = %20.10f A " % zlen, file=f)
print("#", file=f)
for atom in atoms:
itype = int(atom[1])
xfrac = (atom[2]-box[0])/xlen
yfrac = (atom[3]-box[1])/ylen
zfrac = (atom[4]-box[2])/zlen
# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
# print("1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]), file=f)
print("1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
print time,
print(time)
sys.stdout.flush()
f.close()
n += 1
print "\nwrote %s snapshots in CFG format" % n
print("\nwrote %s snapshots in CFG format" % n)
# --------------------------------------------------------------------
@ -163,25 +165,25 @@ class cfg:
ylen = box[4]-box[1]
zlen = box[5]-box[2]
print >>f,"Number of particles = %d " % len(atoms)
print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
print >>f,"H0(1,1) = %20.10f A " % xlen
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(2,2) = %20.10f A " % ylen
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(3,3) = %20.10f A " % zlen
print >>f,"#"
print("Number of particles = %d " % len(atoms), file=f)
print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
print("H0(1,1) = %20.10f A " % xlen, file=f)
print("H0(1,2) = 0.0 A ", file=f)
print("H0(1,3) = 0.0 A ", file=f)
print("H0(2,1) = 0.0 A ", file=f)
print("H0(2,2) = %20.10f A " % ylen, file=f)
print("H0(2,3) = 0.0 A ", file=f)
print("H0(3,1) = 0.0 A ", file=f)
print("H0(3,2) = 0.0 A ", file=f)
print("H0(3,3) = %20.10f A " % zlen, file=f)
print("#", file=f)
for atom in atoms:
itype = int(atom[1])
xfrac = (atom[2]-box[0])/xlen
yfrac = (atom[3]-box[1])/ylen
zfrac = (atom[4]-box[2])/zlen
# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
# print("1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]), file=f)
print("1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
f.close()