# Now we need to add the symmetry vector * the strain.
# For this, we need to identify which struct positions correspond
# to which position in the posvec output by FROZSL,
# and apply the corresponding symvec * strain.
struct = Structure("POSCAR_X3-")
for refposnum in range(len(struct.positions)):
for posnum in range(len(posvec)):
if vectorEqual(posvec[posnum], struct.positions[refposnum], 1e-4):
print "Found the position to move."
struct.positions[refposnum] = struct.positions[refposnum] + p4mat.Vector(symvec[posnum].tolist()) * strain
print "New positions: "
print struct.positions
struct.write("POSCAR_"+name+"_u_"+repr(strain), newformat=0)
if runflag:
# run the calculation
vaspcmd = 'mr vasp'
os.system("cp POSCAR_"+name+"_u_"+repr(strain)+" POSCAR")
os.system("more POSCAR")
os.system(vaspcmd)
os.system('cp vasprun.xml vasprun_'+name+'_u_'+repr(strain)+'.xml')
os.system('cp OUTCAR OUTCAR_'+name+'_u_'+repr(strain))
os.system('cp CHGCAR CHGCAR_'+name+'_u_'+repr(strain))
currentrun = XMLSystemPM('vasprun.xml')
currentenergy = currentrun.FREE_ENERGY
os.system(" E=`tail -n 2 OSZICAR` ; echo " + ("%1.8g" % strain) + " $E >> frozen_phonon.out")
outfile.write(repr(strain)+' '+repr(currentenergy)+'\n')
# For this, we need to identify which struct positions correspond
# to which position in the posvec output by FROZSL,
# and apply the corresponding symvec * strain.
struct = Structure("POSCAR_X3-")
for refposnum in range(len(struct.positions)):
for posnum in range(len(posvec)):
if vectorEqual(posvec[posnum], struct.positions[refposnum], 1e-4):
print "Found the position to move."
struct.positions[refposnum] = struct.positions[
refposnum] + p4mat.Vector(symvec[posnum].tolist()) * strain
print "New positions: "
print struct.positions
struct.write("POSCAR_" + name + "_u_" + repr(strain), newformat=0)
if runflag:
# run the calculation
vaspcmd = 'mr vasp'
os.system("cp POSCAR_" + name + "_u_" + repr(strain) + " POSCAR")
os.system("more POSCAR")
os.system(vaspcmd)
os.system('cp vasprun.xml vasprun_' + name + '_u_' + repr(strain) +
'.xml')
os.system('cp OUTCAR OUTCAR_' + name + '_u_' + repr(strain))
os.system('cp CHGCAR CHGCAR_' + name + '_u_' + repr(strain))
currentrun = XMLSystemPM('vasprun.xml')
currentenergy = currentrun.FREE_ENERGY
os.system(" E=`tail -n 2 OSZICAR` ; echo " + ("%1.8g" % strain) +
from p4vasp.db import *
from p4vasp.Structure import Structure
from sys import stdout
db = getDatabase()[0]
db.connect()
db.addUser()
path = "XDATCAR"
s = Structure(path)
s.write(stdout)
f = open(path)
for i in range(8):
f.readline() #Skip header
db.addRecord(keywords="MD,XDATCAR", name=s.comment)
step = 0
while 1:
for i in range(len(s)):
s[i] = map(float, f.readline().split())
step += 1
#s.write(stdout)
db.storeStructure(s, step)
if f.readline().strip() != "":
break