def readmps(self, filename):
line1 = False
line2 = False
conversion = False
d = None
quad = None
q = None
r = None
element = None
with open(filename, "r") as f:
for line in f.readlines():
a = line.split()
if "Units angstrom" in line:
conversion = 1
elif "Units bohr" in line:
conversion = 0.52917721092
elif "Rank" in line:
#print line
element = a[0]
rank = int(a[5])
if conversion != False:
r = conversion * np.array(a[1:4], dtype=float)
line1 = True
elif len(a) == 1 and line1:
q = float(a[0])
line2 = True
elif len(a) == 3 and line1 and line2:
d = np.array(a[0:3], dtype=float)
line3 = True
elif len(
a
) == 5 and line1 and line2 and line3 and "P" not in line:
quad = np.array(a[0:], dtype=float)
line3 = True
elif "P" in line and line1 and line2:
p = np.array(a[1:], dtype=float)
#print p
ptensor = np.array([[p[0], p[1], p[2]], [p[1], p[3], p[4]],
[p[2], p[4], p[5]]])
line1 = False
line2 = False
line3 = False
at = atom(element, r)
if quad == None:
quad = np.zeros(5)
if d == None:
d = np.zeros(3)
at.setmultipoles(q, d, quad, ptensor)
self.updateatom(at)
self.calccoG()
return
def readmps(self,filename):
line1=False
line2=False
conversion=False
d=None
quad=None
q=None
r=None
element=None
with open(filename,"r") as f:
for line in f.readlines():
a=line.split()
if "Units angstrom" in line:
conversion=1
elif "Units bohr" in line:
conversion=0.52917721092
elif "Rank" in line:
#print line
element=a[0]
rank=int(a[5])
if conversion!=False:
r=conversion*np.array(a[1:4],dtype=float)
line1=True
elif len(a)==1 and line1:
q=float(a[0])
line2=True
elif len(a)==3 and line1 and line2:
d=np.array(a[0:3],dtype=float)
line3=True
elif len(a)==5 and line1 and line2 and line3 and "P" not in line:
quad=np.array(a[0:],dtype=float)
line3=True
elif "P" in line and line1 and line2:
p=np.array(a[1:],dtype=float)
#print p
ptensor=np.array([[p[0],p[1],p[2]],[p[1],p[3],p[4]],[p[2],p[4],p[5]]])
line1=False
line2=False
line3=False
at=atom(element,r)
if quad==None:
quad=np.zeros(5)
if d==None:
d=np.zeros(3)
at.setmultipoles(q,d,quad,ptensor)
self.updateatom(at)
self.calccoG()
return
def readxyzfile(self,filename):
noofatoms=None
with open(filename,"r") as f:
for line in f.readlines():
if line[0]=="#":
continue
entries=line.split()
if len(entries)==0:
continue
elif len(entries)==1:
noofatoms=int(entries[0])
elif len(entries)==4:
name=entries[0]
pos=np.array(entries[1:],dtype=float)
self.atomlist.append(atom(name,pos))
self.calccoG()
return
def readxyzfile(self, filename):
noofatoms = None
with open(filename, "r") as f:
for line in f.readlines():
if line[0] == "#":
continue
entries = line.split()
if len(entries) == 0:
continue
elif len(entries) == 1 and RepresentsInt(entries[0]):
noofatoms = int(entries[0])
elif len(entries) != 4 or (not RepresentsFloat(entries[1])
or not RepresentsFloat(entries[2])
or not RepresentsFloat(entries[3])):
self.name = line
elif len(entries) == 4:
name = entries[0]
pos = np.array(entries[1:], dtype=float)
self.atomlist.append(atom(name, pos))
self.calccoG()
return