def readStructure(self, Id, cstructure=False):
s = Structure()
l = self.fetchone(
"""SELECT calc_id,scale,comment,a11,a12,a13,a21,a22,a23,a31,a32,a33,
species FROM #STRUCT WHERE id=%d""" % (Id))
(calc_id, scale, s.comment, s.basis[0][0], s.basis[0][1],
s.basis[0][2], s.basis[1][0], s.basis[1][1], s.basis[1][2],
s.basis[2][0], s.basis[2][1], s.basis[2][2], spec) = l
s.scaling = [scale]
s.setCartesian()
l = self.fetchall(
"SELECT specie,element,x,y,z FROM #STRUCTPOS WHERE structure_id=%d ORDER BY atomnumber"
% (Id))
for spec, element, x, y, z in l:
i = s.appendAtom(spec, Vector(x, y, z))
s.info.getRecordForAtom(i).element = str(element)
l = self.fetchall(
"SELECT x,y,z FROM #STRUCTCONSTRAINTS WHERE structure_id=%d ORDER BY atomnumber"
% (Id))
if len(l):
s.setSelective()
for i in range(len(l)):
s.selective[i] = [int(l[i][0]), int(l[i][1]), int(l[i][2])]
if cstructure:
s = p4vasp.cStructure.Structure(s)
return s
def storeStructure(self, s, step=None):
calc_id = self.calc_id
if calc_id is not None and step is not None:
for l in self.fetchall(
"SELECT id FROM #STRUCT WHERE calc_id=%d AND step=%d" %
(calc_id, step)):
removeStructure(db, l[0])
info = s.info
if len(s.scaling) != 1:
s.correctScaling()
cmd = "%s, %s," % (von(calc_id), von(step))
cmd += "%14.12f,'%s'," % (s.scaling[0], s.comment)
cmd += """%14.12f,%14.12f,%14.12f,
%14.12f,%14.12f,%14.12f,
%14.12f,%14.12f,%14.12f,%d""" % (
s.basis[0][0], s.basis[0][1], s.basis[0][2], s.basis[1][0],
s.basis[1][1], s.basis[1][2], s.basis[2][0], s.basis[2][1],
s.basis[2][2], s.types)
Id = self.insertRecord(
"#STRUCT", "id",
"calc_id, step, scale,comment,a11,a12,a13,a21,a22,a23,a31,a32,a33,species",
cmd)
if s.isSelective():
sel = s.selective
for i in range(len(sel)):
self.exe(
"""INSERT INTO #STRUCTCONSTRAINTS (structure_id,calc_id,atomnumber,x,y,z)
VALUES (%d,%s,%d,%d,%d,%d)""" %
(Id, von(calc_id), i, sel[i][0], sel[i][1], sel[i][2]))
sc = Structure()
sc.setStructure(s)
sc.setCartesian()
for i in range(len(s)):
si = s.speciesIndex(i)
self.exe(
"""INSERT INTO #STRUCTPOS (structure_id,calc_id,atomnumber,specie,element,x,y,z)
VALUES (%d,%s,%d,%d,'%s',%14.12f,%14.12f,%14.12f)""" %
(Id, von(calc_id), i, si, info[si].element, sc[i][0], sc[i][1],
sc[i][2]))
self.commit()
return Id