def check1(self,filename='FORCE_CONSTANTS'):
from lxml import etree
from ase import io
ref=io.read('SPOSCAR')
fc2=readfc2(filename)
np.set_printoptions(precision=2,suppress=True)
files=['dir_POSCAR-001']
vasprunxml="dir_SPOSCAR/vasprun.xml"
if exists(vasprunxml):
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces0=self.parseVasprun(vasprun,'forces')
print forces0.max()
else:
forces0=0.0
for file in files:
print file
POSCAR='dirs/%s/POSCAR'%file
vasprunxml="dirs/%s/vasprun.xml"%file
atoms=io.read(POSCAR)
u=atoms.positions-ref.positions
f=-np.einsum('ijkl,jl',fc2,u)
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces=self.parseVasprun(vasprun,'forces')-forces0
print np.abs(f).max(),"\n"
print np.abs(forces-f).max()
print np.allclose(f,forces,atol=1e-2)
def check(self,filename='FORCE_CONSTANTS'):
try:
from lxml import etree
except ImportError:
print "You need to install python-lxml."
from ase import io
ref=io.read('SPOSCAR')
files=shell_exec("ls dirs").split('\n')
fc2=readfc2(filename)
np.set_printoptions(precision=2,suppress=True)
vasprunxml="dir_SPOSCAR/vasprun.xml"
if exists(vasprunxml):
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces0=self.parseVasprun(vasprun,'forces')
print forces0.max()
else:
forces0=0.0
for file in files:
print file
POSCAR='dirs/%s/POSCAR'%file
vasprunxml="dirs/%s/vasprun.xml"%file
atoms=io.read(POSCAR)
u=atoms.positions-ref.positions
f=-np.einsum('ijkl,jl',fc2,u)
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces=self.parseVasprun(vasprun,'forces')-forces0
print np.abs(f).max(),"\n"
print np.abs(forces-f).max()
print np.allclose(f,forces,atol=1e-2)
def fc(self, dir, mm):
fc = readfc2(dir + '/FORCE_CONSTANTS')
atoms = read(dir + '/POSCAR')
fc = self.nomalizeFC(fc, mm, atoms)
fc = self.rearangefc(fc, atoms, dir)
return fc
def stub(self):
files=shell_exec("ls dirs").split('\n')
files=map(lambda x:x.replace('dir_',''),files)
fc2=readfc2('fc2')
for file in files:
from ase import io
ref=io.read('SPOSCAR')
a='dirs/dir_'+str(file)
atoms=io.read(a+"/POSCAR")
u=atoms.positions-ref.positions
f=-np.einsum('ijkl,jl',fc2,u)
forces=""
for force in f:
forces+="<v> %f %f %f </v>\n"%tuple(force)
vasprun='<root><calculation><varray name="forces" >\n'
vasprun+=forces
vasprun+='</varray></calculation></root>\n'
write(vasprun,a+"/vasprun.xml")
def getjvhar():
allpos = np.load('allpos.npy')
atoms = io.read("POSCAR")
n = len(atoms)
m = len(allpos)
from aces.f import readfc2
fc2 = readfc2()
sigmas_haR = np.zeros([m, n, 3, 3])
R = allpos
dR = R - np.einsum('i,jk', np.ones(m), atoms.positions)
dRI = np.einsum('ijk,l', dR, np.ones(n))
dRJ = np.einsum('ilkj', dRI)
RI = np.einsum('ijk,l', R, np.ones(n))
RJ = np.einsum('ilkj', RI)
sigmas_haR = .5 * np.einsum('ijab,tiaj,tibj->tiab',
fc2, dRI - dRJ, RI - RJ)
v = np.gradient(allpos)[0]
jv_haR = np.einsum('ijkl,ijl->ik', sigmas_haR, v)
np.save('jv_haR.npy', jv_haR)
def getjvhar():
allpos = np.load('allpos.npy')
atoms = io.read("POSCAR")
n = len(atoms)
m = len(allpos)
from aces.f import readfc2
fc2 = readfc2()
sigmas_haR = np.zeros([m, n, 3, 3])
R = allpos
dR = R - np.einsum('i,jk', np.ones(m), atoms.positions)
dRI = np.einsum('ijk,l', dR, np.ones(n))
dRJ = np.einsum('ilkj', dRI)
RI = np.einsum('ijk,l', R, np.ones(n))
RJ = np.einsum('ilkj', RI)
sigmas_haR = .5 * np.einsum('ijab,tiaj,tibj->tiab', fc2, dRI - dRJ,
RI - RJ)
v = np.gradient(allpos)[0]
jv_haR = np.einsum('ijkl,ijl->ik', sigmas_haR, v)
np.save('jv_haR.npy', jv_haR)