def receiveTarget(self):
self.clientSock.send("receivingTarget")
data = self.clientSock.recv(1024)
self.clientSock.send("targetReceived")
radecS = data.split(":")
Ra = Angle(r=float(radecS[0]))
Dec = Angle(r=float(radecS[1]))
return [Ra, Dec]
def test_angle_class_hms_and_dms_must_be_consistent():
a = Angle(d=1)
a.dms = (1, 1, 0, 0)
assert a.hms.hms == (1, 0, 4, 0.0)
a.hms = (1, 1, 0, 0)
assert a.dms.dms == (1, 15, 0, 0.0)
def test_angle_class_hms_and_dms_must_be_consistent():
a = Angle(d=1)
a.dms = (1, 1, 0, 0)
assert a.hms.hms == (1, 0, 4, 0.0)
a.hms = (1, 1, 0, 0)
assert a.dms.dms == (1, 15, 0, 0.0)
def correct(self,Az,Alt):
tVec = self.AzAltToVec(Az.r, Alt.r)
tV = np.matrix([tVec])
dVec = self.rotationMatrix*tV.T
[rAz, rAlt] = self.VecToAzAlt(dVec)
aAz = Angle(r=rAz)
aAlt = Angle(r=rAlt)
return [aAz,aAlt]
def __init__(self, parent=None):
super().__init__(parent)
self.offset = 75
self.span = self.offset + 525
self.center = QPoint(self.span / 2, self.span / 2)
self.setMinimumSize(self.span, self.span)
self.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Maximum)
self.setMouseTracking(True)
self.wedges = []
for start in range(0, 360 * 16, 45 * 16):
self.wedges.append(
CompassWedge(
start, self.span, self.span, self.offset,
Angle(floor(((360 - start / 16 + 45) % 360) / 45)), self))
deg_font = QFont("Consolas", 22, 2)
for deg in range(8):
temp = QLabel(self)
angle = deg * 45
temp.setText(str(angle) + '°')
temp.setFont(deg_font)
tw = temp.fontMetrics().boundingRect(temp.text()).width()
th = temp.fontMetrics().boundingRect(temp.text()).height()
temp.move(self.deg_lbl_pos((180 - angle) % 360, QSize(tw, th)))
def __init__(self, upCalibration, downCalibration):
self.upCalibration = upCalibration
self.downCalibration = downCalibration
self.lastPosition = Angle(d=0)
self.ascending = True
self.voltageRecord = [0, 0]
self.buffer = 0.0002
def voltageToAngle(self, volts):
power = 0
degrees = 0
for c in reversed(self.coeficients):
degrees += math.pow(volts, power) * c
power += 1
return (Angle(d=degrees))
def test_angle_class_getting_hms_property_must_work():
a = Angle(d=45.0)
assert a.hms.sign == 1
assert a.hms.hh == 3.0
assert a.hms.mm == 0.0
assert a.hms.ss == 0.0
assert a.hms.hms == (1, 3, 0.0, 0.0)
assert str(a.hms) == ("+03HH 00MM 00.000SS")
a = Angle(sg="-12h14m13.567s")
assert a.hms.sign == -1
assert a.hms.hh == 12
assert a.hms.mm == 14
assert a.hms.ss == 13.567
assert a.hms.hms == (-1, 12, 14, 13.567)
assert str(a.hms) == "-12HH 14MM 13.567SS"
def test_angle_class_getting_dms_property_must_work():
a = Angle(d=45.0)
assert a.dms.sign == 1
assert a.dms.dd == 45.0
assert a.dms.mm == 0.0
assert a.dms.ss == 0.0
assert a.dms.dms == (1, 45, 0.0, 0.0)
assert str(a.dms) == ("+45DD 00MM 00.000SS")
a = Angle(sg="-12h14m13.567s")
assert a.dms.sign == -1
assert a.dms.dd == 183
assert a.dms.mm == 33
assert a.dms.ss == 23.505
assert a.dms.dms == (-1, 183, 33, 23.505)
assert str(a.dms) == "-183DD 33MM 23.505SS"
def test_angle_class_setting_hms_property_must_work():
a = Angle(d=0.0)
a.hms = (1, 12, 14, 13.567)
v = 12 + 14 / 60.0 + 13.567 / 3600.0
assert a.h == v
assert a.hms.sign == 1
assert a.hms.hh == 12
assert a.hms.mm == 14
assert a.hms.ss == 13.567
assert str(a.hms) == "+12HH 14MM 13.567SS"
a.hms.hh = 15
assert a.h == 15 + 14 / 60.0 + 13.567 / 3600.0
a.hms.mm = 15
assert a.h == 15 + 15 / 60.0 + 13.567 / 3600.0
a = Angle(d=0.0)
a.hms.mm = 12
assert round(a.h, 15) == 12 / 60.0
def test_angle_class_setting_dms_property_must_work():
a = Angle(d=0.0)
a.dms = (-1, 183, 33, 23.505)
v = -1 * (183 + 33 / 60.0 + 23.505 / 3600.0)
assert a.d == v
assert a.dms.sign == -1
assert a.dms.dd == 183
assert a.dms.mm == 33
assert a.dms.ss == 23.505
assert str(a.dms) == "-183DD 33MM 23.505SS"
a.dms.dd = 101
assert a.d == -101.55652916666668
a.dms.mm = 15
assert a.d == -101.25652916666667
a = Angle(d=0.0)
a.dms.mm = 12
assert round(a.d, 15) == 12 / 60.0
def test_angle_class_setting_dms_property_must_work():
a = Angle(d=0.0)
a.dms = (-1, 183, 33, 23.505)
v = -1 * (183 + 33/60.0 + 23.505/3600.0)
assert a.d == v
assert a.dms.sign == -1
assert a.dms.dd == 183
assert a.dms.mm == 33
assert a.dms.ss == 23.505
assert str(a.dms) == "-183DD 33MM 23.505SS"
a.dms.dd = 101
assert a.d == -101.55652916666668
a.dms.mm = 15
assert a.d == -101.25652916666667
a = Angle(d=0.0)
a.dms.mm = 12
assert round(a.d, 15) == 12/60.0
def test_angle_class_setting_hms_property_must_work():
a = Angle(d=0.0)
a.hms = (1, 12, 14, 13.567)
v = 12 + 14/60.0 + 13.567/3600.0
assert a.h == v
assert a.hms.sign == 1
assert a.hms.hh == 12
assert a.hms.mm == 14
assert a.hms.ss == 13.567
assert str(a.hms) == "+12HH 14MM 13.567SS"
a.hms.hh = 15
assert a.h == 15 + 14/60.0 + 13.567/3600.0
a.hms.mm = 15
assert a.h == 15 + 15/60.0 + 13.567/3600.0
a = Angle(d=0.0)
a.hms.mm = 12
assert round(a.h, 15) == 12/60.0
def test_angle_class_must_initialize_properly():
a = Angle(sg="12h14m13.567s")
val = 12 + 14 / 60.0 + 13.567 / 3600.0
assert a.h == val
assert a.ounit == 'hours'
assert a.r == h2r(val)
assert a.d == h2d(val)
assert a.arcs == h2arcs(val)
# ignore r
with pytest.warns(UserWarning):
Angle(sg="12h14m13.567s", r=10)
a = Angle(sg="12h14m13.567s", r=10)
assert a.r == h2r(val)
assert a.ounit == 'hours'
# ignore h and mm
with pytest.warns(UserWarning):
a = Angle(r=10, h=20)
a = Angle(r=10, h=20)
assert a.r == 10
assert a.ounit == 'radians'
assert a.h == r2h(10)
a = Angle(h=20, d=10)
assert a.d == 10
assert a.ounit == 'degrees'
assert a.h == d2h(10)
def loadProjParams(projName):
"""
This function loads projections.txt file, which includes different
projections with their correspoding parameters. A sample raw of this
file has the following format:
TM3-EAST, TM, BESSEL, 0.9999, 34, 26:42:58.815, 200000, 0
where each comma delimited value corresponds to:
projID, projFamily, ellipsoid, scale, lat0, lon0, falseEasting,
falseNorthing respectively.
It should be stated here that lat0, lon0 are defined in degrees
(dms format, e.g. -0:23:9.01239573) within file.
Arguments
projName: string that specifies projection's ID,
could be one of the followings:
'TM3-WEST', 'TM3-CENTRAL', 'TM3-EAST', 'TM87',
'UTM-34N', 'UTM-35N', 'HATT', 'TM87-WGS84'
* If user desires to add another projection has to modify
projections.txt file following its header's instructions
Returns
dictionary of projection's parameters, i.e.
{'projID': string, 'projFamily': string, 'ellipsoid': string,
'scale': number, 'lat0': number, 'lon0': number,
'falseEasting': number, 'falseNorthing': number}
* values of dictionary could be None if they are missing from file
* CAUTION. lat0, lon0 inserted as degrees in dms format but returned
in radians
"""
with open("projections.txt") as fObj:
readCSV = reader(fObj, delimiter=',')
header = [value.strip() for value in next(readCSV)]
projParams = dict.fromkeys(header)
for line in readCSV:
if line[0].strip() == projName:
for key, value in zip(header, line):
projParams[key] = value.strip()
for key in ['scale', 'falseEasting', 'falseNorthing']:
if projParams[key]:
projParams[key] = float(projParams[key])
for key in ['lat0', 'lon0']:
if projParams[key]:
# projParams[key] = DMStoRads(projParams[key])
projParams[key] = Angle(projParams[key])
return projParams
raise Exception("The projection you defined does not exist "
"in projections.txt file")
def setAngleMenu(self, angleName):
while (True):
print "** Enter %s\n" % angleName
print "** Use one of the following formats:"
print "** Option 1: Degrees \"D\" e.g. 15.1275"
print "** Option 2: Degrees:Minutes \"DD:M\" e.g. 15:7.65"
print "** Option 3: Degrees:Minutes:Seconds \"DD:MM:SS\" e.g. 15:07:39"
print "** %s:" % angleName
uInput = raw_input()
try:
theAngle = Angle(uInput)
return theAngle
break
except ValueError as e:
print "There was an error in the angle value that you entered: %s" % e.message
def invTM(E, N, projection):
"""
geodetic values in radians
ellipsoid of class Ellipsoid
m0 scale factor
E0, N0 false Easting, Northing in meters
returns projected coordinates of a point in meters
"""
ellipsoid = projection.ellipsoid
m0 = projection.m0
lat0 = projection.lat0.radians
lon0 = projection.lon0.radians
E0 = projection.E0
N0 = projection.N0
S = N / m0
lat = latFromMeridianLength(lat0, S, ellipsoid)
t = tan(lat)
hta2 = ellipsoid.ePrimeSquared * (cos(lat)**2)
E = E - E0
W = sqrt(1 - ellipsoid.eSquared * (sin(lat))**2)
N = ellipsoid.a / W
Q = E / (m0 * N)
M = ellipsoid.a * (1 - ellipsoid.eSquared) / (W**3)
T10 = t / (2 * m0**2 * M * N)
T11 = (t / (24 * m0**4 * M * N**3)) *\
(5 + (3 * t**2) + hta2 - (4 * hta2**2) - (9 * t**2 * hta2))
T12 = (t / (720 * m0**6 * M * N**5)) *\
(61 + (90 * t**2) + (45 * t**4) + (46 * hta2) - (252 * t**2 * hta2) -
(3 * hta2**2) + (100 * hta2**3) - (66 * t**2 * hta2**2) -
(90 * t**4 * hta2) + (88 * hta2**4) + (225 * t**4 * hta2**2) +
(84 * t**2 * hta2**3) - (192 * t**2 * hta2**4))
T13 = (t / (40320 * m0**8 * M * N**7)) *\
(1385 + (3633 * t**2) + (4095 * t**4) + (1575 * t**6))
T14 = 1 / cos(lat)
T15 = (1 + (2 * t**2) + hta2) / (6 * cos(lat))
T16 = (5 + (6 * hta2) + (28 * t**2) - (3 * hta2**2) + (8 * t**2 * hta2) +
(24 * t**4) - (4 * hta2**3) + (4 * t**2 * hta2**2) +
(24 * t**2 * hta2**3)) / (120 * cos(lat))
T17 = (61 + (66 * t**2) + (1320 * t**4) + (720 * t**6)) / 5040
lat = lat - (T10 * E**2) + (T11 * E**4) - (T12 * E**6) + (T13 * E**8)
lon = lon0 + (T14*Q) - (T15 * Q**3) + (T16 * Q**5) - (T17 * Q**7)
lat = Angle(lat)
lat.angleType = 'dms'
lon = Angle(lon)
lon.angleType = 'dms'
return lat, lon
def log_item(self, data):
last_unlogged = self.timeout_timer.isActive()
self.timeout_timer.start()
src = self.sender()
if type(src) is ActionsWidget:
if self.exact_angle.has_valid():
if self.exact_angle.is_valid():
self.log_angle(self.exact_angle.calc_angle())
self.exact_angle.clear_state()
if src.source is LogSource.SYSTEM:
self.log_system(src.get_action(data))
if last_unlogged:
self.update_temp_log()
elif src.source is LogSource.EVENT:
self.log_event(src.get_action(data))
elif type(src) is Compass:
self.log_compass(Angle.to_string(data))
elif type(src) is ExactAngle:
self.log_angle(str(data))
def test_angle_class_must_handle_assignments():
a = Angle(d=10.5)
a.r = d2r(45.0)
v = 45.0
assert a.r == d2r(v)
assert a.h == d2h(v)
assert a.arcs == d2arcs(v)
assert a.ounit == 'degrees'
v = 46.0
# assignment
a.r = d2r(v)
assert a.r == d2r(v)
assert a.h == d2h(v)
assert a.d == v
assert a.arcs == d2arcs(v)
assert a.ounit == 'degrees' # no change
v = 49.0
a.d = v
assert a.r == d2r(v)
assert a.h == d2h(v)
assert a.d == v
assert a.arcs == d2arcs(v)
assert a.ounit == 'degrees' # no change
v = 10
a.h = v
assert a.r == h2r(v)
assert a.h == v
assert a.d == h2d(v)
assert a.arcs == h2arcs(v)
assert a.ounit == 'degrees' # no change
v = 3600.0
a.arcs = v
assert a.r == arcs2r(v)
assert a.h == arcs2h(v)
assert a.d == arcs2d(v)
assert a.arcs == v
assert a.ounit == 'degrees' # no change
def test_angle_class_must_handle_assignments():
a = Angle(d=10.5)
a.r = d2r(45.0)
v = 45.0
assert a.r == d2r(v)
assert a.h == d2h(v)
assert a.arcs == d2arcs(v)
assert a.ounit == 'degrees'
v = 46.0
# assignment
a.r = d2r(v)
assert a.r == d2r(v)
assert a.h == d2h(v)
assert a.d == v
assert a.arcs == d2arcs(v)
assert a.ounit == 'degrees' # no change
v = 49.0
a.d = v
assert a.r == d2r(v)
assert a.h == d2h(v)
assert a.d == v
assert a.arcs == d2arcs(v)
assert a.ounit == 'degrees' # no change
v = 10
a.h = v
assert a.r == h2r(v)
assert a.h == v
assert a.d == h2d(v)
assert a.arcs == h2arcs(v)
assert a.ounit == 'degrees' # no change
v = 3600.0
a.arcs = v
assert a.r == arcs2r(v)
assert a.h == arcs2h(v)
assert a.d == arcs2d(v)
assert a.arcs == v
assert a.ounit == 'degrees' # no change
def ECEFtoGeodetic(X, Y, Z, ellipsoid):
"""
X, Y, Z in meters
ellipsoid: class ellipsoid
returns Geodetic lat, lon in Angle and h in meters
"""
lon = atan2(Y, X)
P = sqrt(X**2 + Y**2)
lat0 = atan2((Z * (1 + ellipsoid.ePrimeSquared)), P)
dlat = 1
while dlat > 10**-12:
W = sqrt(1 - ellipsoid.eSquared * (sin(lat0))**2)
N = ellipsoid.a / W
lat = atan2((Z + ellipsoid.eSquared * N * sin(lat0)), P)
dlat = abs(lat - lat0)
lat0 = lat
h = (Z / sin(lat)) - ((1 - ellipsoid.eSquared) * N)
lat = Angle(lat)
lat.angleType = 'dms'
lon = Angle(lon)
lon.angleType = 'dms'
return lat, lon, h
def getLatLon(self):
uLat = self.getGeneric('location', 'latitude')
Lat = Angle(r=float(uLat))
uLon = self.getGeneric('location', 'longitude')
Lon = Angle(r=float(uLon))
return [Lat,Lon]
def main():
"""
This test shows various operators within Angle and AngleContainer classes.
Shows memory management structure and access methods
"""
p1 = Particle([1.1, 1.1, 1.1], "Si", 2.0, 1.23)
p2 = Particle([2.2, 2.2, 2.2], "Si", 1.0, 2.34)
p3 = Particle([3.3, 3.3, 3.3], "Si", 1.0, 2.34)
#
p4 = Particle([4.4, 4.4, 4.4], "C", 1.0, 2.34) # ptcl 1
p5 = Particle([5.5, 5.5, 5.5], "C", 1.0, 2.34) # ptcl 2
p6 = Particle([6.6, 6.6, 6.6], "C", 1.0, 2.34) # ptcl 3
b1 = Bond(1, 2, 1.11, "hooke")
b2 = Bond(2, 3, 2.22, "hooke")
#
b3 = Bond(1, 2, 3.33, "hooke")
b4 = Bond(2, 3, 4.44, "hooke")
a1 = Angle(1, 2, 3, 1.11, "harmonic")
#
a2 = Angle(1, 2, 3, 2.22, "harmonic")
atoms1 = ParticleContainer()
atoms2 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
#
atoms2.put(p4)
atoms2.put(p5)
atoms2.put(p6)
bonds1 = BondContainer()
bonds2 = BondContainer()
bonds1.put(b1)
bonds1.put(b2)
bonds2.put(b3)
bonds2.put(b4)
angles1 = AngleContainer()
angles2 = AngleContainer()
angles1.put(a1)
angles2.put(a2)
del p1, p2, p3, p4, p5, p6, b1, b2, b3, b4, a1, a2
print "\n Cleaning memory for initial objects \n"
print "angles1 container"
print angles1
print " "
print "angles2 container"
print angles2
print "Testing 'in' operator (1 in angles1)"
if (1 in angles1):
print "angles1 contains gid 1"
else:
print "key not found in angles1"
print "Testing 'in' operator (5 in angles1)"
if (5 in angles1):
print "angles1 contains gid 5"
else:
print "key not found in angles1"
print " "
angles1 += angles2
print "Will print the new angles1 after adding angles1 += angles2"
print angles1
print "Check for pre-existing angle"
if angles1.hasAngle([3, 2, 1]):
print "angle 1--2--3 exists"
else:
print "angle 1--2--3 does NOT exists"
print "Check for pre-existing angle"
if angles1.hasAngle([2, 3, 1]):
print "angle 2--3--1 exists"
else:
print "angle 2--3--1 does NOT exists"
def main():
"""
Illustrates how a substructure method returns subgroup with ONLY particle container included
This is for speed considerations
"""
print "**********************************************************************************************"
print "Illustrates how a substructure method returns subgroup with ONLY particle container included"
print "This is for speed considerations"
print "**********************************************************************************************\n"
p1 = Particle([1.1, 1.1, 1.1], "Si", 2.0, 1.23)
p2 = Particle([2.2, 2.2, 2.2], "Si", 1.0, 2.34)
p3 = Particle([3.3, 3.3, 3.3], "Si", 1.0, 2.34)
p4 = Particle([4.4, 4.4, 4.4], "Si", 1.0, 2.34)
p5 = Particle([5.5, 5.5, 5.5], "C", 1.0, 2.34) # 1
p6 = Particle([6.6, 6.6, 6.6], "C", 1.0, 2.34) # 2
p7 = Particle([7.7, 7.7, 7.7], "C", 1.0, 2.34) # 3
p8 = Particle([8.8, 8.8, 8.8], "C", 1.0, 2.34) # 4
b1 = Bond(1, 2, 1.11, "hooke")
b2 = Bond(2, 3, 2.22, "hooke")
b3 = Bond(3, 4, 3.33, "hooke")
b4 = Bond(4, 5, 4.44, "hooke")
b5 = Bond(5, 6, 5.55, "hooke")
b6 = Bond(6, 7, 6.66, "hooke")
b7 = Bond(7, 8, 7.77, "hooke")
a1 = Angle(1, 2, 3, 1.11, "harmonic")
a2 = Angle(2, 3, 4, 2.22, "harmonic")
a3 = Angle(3, 4, 5, 3.33, "harmonic")
a4 = Angle(4, 5, 6, 4.44, "harmonic")
a5 = Angle(5, 6, 7, 5.55, "harmonic")
a6 = Angle(6, 7, 8, 6.66, "harmonic")
d1 = Dihedral(1, 2, 3, 4, 1.11, "stiff")
d2 = Dihedral(2, 3, 4, 5, 2.22, "stiff")
d3 = Dihedral(3, 4, 5, 6, 3.33, "stiff")
d4 = Dihedral(4, 5, 6, 7, 4.44, "stiff")
d5 = Dihedral(5, 6, 7, 8, 5.55, "stiff")
atoms1 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
atoms1.put(p4)
atoms1.put(p5)
atoms1.put(p6)
atoms1.put(p7)
atoms1.put(p8)
bonds = BondContainer()
bonds.put(b1)
bonds.put(b2)
bonds.put(b3)
bonds.put(b4)
bonds.put(b5)
bonds.put(b6)
bonds.put(b7)
angles = AngleContainer()
angles.put(a1)
angles.put(a2)
angles.put(a3)
angles.put(a4)
angles.put(a5)
angles.put(a6)
dihedrals = DihedralContainer()
dihedrals.put(d1)
dihedrals.put(d2)
dihedrals.put(d3)
dihedrals.put(d4)
dihedrals.put(d5)
del p1, p2, p3, p4, p5, p6, p7, p8
del b1, b2, b3, b4, b5, b6, b7
del a1, a2, a3, a4, a5, a6
del d1, d2, d3, d4, d5
polymer1 = StructureContainer(atoms1, bonds, angles, dihedrals)
del atoms1, bonds, angles, dihedrals
print "********************************************************** \n"
print "polymer1 Structure before returning sub-structure"
print polymer1
print "********************************************************** \n"
print "-------------------------------------------------------------------------------- \n"
print "********************************************************** \n"
print "Testing polymer1.getSubParticleContainer([2,3,4])"
print " currently ID's are reassigned in substructure \n"
subPtclC = polymer1.getSubStructure([2, 3, 4], particlesOnly=True)
print subPtclC
print "********************************************************** \n"
def read_lmpdata( strucC , parmC , data_file):
"""
Read Lammps data file
Arguments:
strucC (StructureContainer)
parmC (ParameterContainer)
data_file (str) data file
ReturnS:
strucC (StructureContainer)
parmC (ParameterContainer)
"""
debug = 0
verbose = True
set_chain_numbers = True
if( not set_chain_numbers ):
print " Warning not reading in chain numbers!!! "
# Load periodic table
pt = periodictable()
F = open(data_file , 'r' )
lines = F.readlines()
F.close()
#
# Read in data header with number of parameters
#
for line in lines:
col = line.split()
if ( len(col) >=2 ):
# Read in number of each topolgical component
if( col[1] == "atoms" ):
n_atoms = int( col[0] )
elif( col[1] == "bonds" ):
n_bonds = int( col[0] )
elif( col[1] == "angles" ):
n_angles = int( col[0] )
elif( col[1] == "dihedrals" ):
n_dihedrals = int( col[0] )
elif( col[1] == "impropers" ):
n_impropers = int( col[0] )
if ( len(col) >= 3 ):
# Read in number of each parameter type
if( col[1] == "atom" and col[2] == "types" ):
n_atypes = int( col[0] )
elif( col[1] == "bond" and col[2] == "types" ):
n_btypes = int( col[0] )
elif( col[1] == "angle" and col[2] == "types" ):
n_angtypes = int( col[0] )
elif( col[1] == "dihedral" and col[2] == "types" ):
n_dtypes = int( col[0] )
elif( col[1] == "improper" and col[2] == "types" ):
n_imptypes = int( col[0] )
# Read in box size
if ( len(col) >= 4 ):
if( col[2] == "xlo" and col[3] == "xhi" ):
strucC.latvec[0][0] = float( col[1] ) - float( col[0] )
if( col[2] == "ylo" and col[3] == "yhi" ):
strucC.latvec[1][1] = float( col[1] ) - float( col[0] )
if( col[2] == "zlo" and col[3] == "zhi" ):
strucC.latvec[2][2] = float( col[1] ) - float( col[0] )
# Prind debug
if( verbose ):
print " atoms ",n_atoms
print " n_bonds ",n_bonds
print " n_angles ",n_angles
print " n_dihedrals ",n_dihedrals
print " n_impropers ",n_impropers
print ""
print "n_atom_types",n_atypes
print "n_bond_types",n_btypes
print "n_angle_types",n_angtypes
print "n_dihedral_types",n_dtypes
print "n_imp_dihedral_types",n_imptypes
# Check to see if a previous read has occured
pt_overwrite = False
if( len(strucC.ptclC) > 0 ):
pt_overwrite = True
# Check of conistent number of atoms
if( pt_overwrite ):
if( len(strucC.ptclC) != n_atoms):
print " %d atoms in passed structure "%(len(strucC.ptclC))
print " %d atoms in data file "%(n_atoms)
sys.exit(" Inconsistent number of atoms " )
else:
#
# Initialize particle container
#
for pid_i in range(n_atoms):
pt_i = Particle( )
strucC.ptclC.put(pt_i)
bonds_overwrite = False
if( len(strucC.bondC) > 0 ):
bonds_overwrite = True
if( len(strucC.bondC) != n_bonds):
print " %d bonds in passed structure "%(len(strucC.bondC))
print " %d bonds in data file "%(n_bonds)
sys.exit(" Inconsistent number of bonds " )
angles_overwrite = False
if( len(strucC.angleC) > 0 ):
angles_overwrite = True
if( len(strucC.angleC) != n_angles):
print " %d angles in passed structure "%(len(strucC.angleC))
print " %d angles in data file "%(n_angles)
sys.exit(" Inconsistent number of angles " )
dih_overwrite = False
if( len(strucC.dihC) > 0 ):
dih_overwrite = True
if( len(strucC.dihC) != n_dihedrals):
print " %d dihedrals in passed structure "%(len(strucC.dihC))
print " %d dihedrals in data file "%(n_dihedrals)
sys.exit(" Inconsistent number of dihedrals " )
imp_overwrite = False
if( len(strucC.impC) > 0 ):
imp_overwrite = True
if( len(strucC.impC) != n_impropers):
print " %d impropers in passed structure "%(len(strucC.impC))
print " %d impropers in data file "%(n_impropers)
sys.exit(" Inconsistent number of impropers " )
#
# Intialize
# - read in boolean to off
#
read_Masses = 0
read_Pair = 0
read_Bond_coeff = 0
read_Angle_coeff = 0
read_Dihedral_coeff = 0
read_Improper_coeff = 0
read_Atoms = 0
read_Bonds = 0
read_Angles = 0
read_Dihedrals = 0
read_Impropers = 0
# - lists as indecise can be out of order in data file
ATYPE_REF = n_atypes*[""]
ATYPE_MASS = np.zeros(n_atypes)
ATYPE_EP = np.zeros(n_atypes)
ATYPE_SIG = np.zeros(n_atypes)
BTYPE_REF = n_btypes*[2*[""]]
BONDTYPE_R0 = np.zeros(n_btypes)
BONDTYPE_K = np.zeros(n_btypes)
ANGTYPE_REF = n_angtypes*[3*[""]]
ANGLETYPE_R0 = np.zeros(n_angtypes)
ANGLETYPE_K = np.zeros(n_angtypes)
DTYPE_REF = n_dtypes*[4*[""]]
DIHTYPE_C = np.zeros((n_dtypes,4))
DIHTYPE_F = np.zeros(n_dtypes)
DIHTYPE_K = np.zeros(n_dtypes)
DIHTYPE_PN = np.zeros(n_dtypes)
DIHTYPE_PHASE = np.zeros(n_dtypes)
IMPTYPE_REF = n_imptypes*[4*[""]]
IMPTYPE_F = np.zeros(n_imptypes)
IMPTYPE_E0 = np.zeros(n_imptypes)
IMPTYPE_K = np.zeros(n_imptypes)
MOLNUMB = n_atoms*[0]
ATYPE_IND = n_atoms*[0]
CHARGES = np.zeros(n_atoms)
R = n_atoms*[np.zeros(3)]
ATYPE = n_atoms*[""]
BONDS = n_bonds*[[0,0]]
BTYPE_IND = n_bonds*[0]
ANGLES = n_angles*[[0,0,0]]
ANGTYPE_IND = n_angles*[0]
DIH = n_dihedrals*[[0,0,0,0]]
DTYPE_IND = n_dihedrals*[0]
#
# Check if values exist and need to be updated or don't and need to be created
#
ljtyp_update = False
ljtyp_cnt = 0
if( len(parmC.ljtypC) > 0 ):
print " LJ types will be updated "
ljtyp_update = True
btyp_update = False
btyp_cnt = 0
if( len(parmC.btypC) > 0 ):
print " Bond types will be updated "
btyp_update = True
atyp_update = False
atyp_cnt = 0
if( len(parmC.atypC) > 0 ):
print " Angle types will be updated "
atyp_update = True
dtyp_update = False
dtyp_cnt = 0
if( len(parmC.dtypC) > 0 ):
print " Dihedral types will be updated "
dtyp_update = True
imptyp_update = False
imptyp_cnt = 0
if( len(parmC.imptypC) > 0 ):
print " Improper dihedrals types will be updated "
imptyp_update = True
#
# Read in data parameters
#
for line in lines:
col = line.split()
if( read_Masses and len(col) >= 2 ):
cnt_Masses += 1
ind = int(col[0]) - 1
ATYPE_MASS[ind] = float(col[1])
if( len(col) >= 4 ):
ATYPE_REF[ind] = col[3]
ptype1 = col[3]
else:
ATYPE_REF[ind] = "??"
ptype1 = "??"
mass_i = float(col[1])
if( ljtyp_update ):
ljtyp_cnt = ind + 1
if( ljtyp_cnt > len(parmC.ljtypC) ):
print "Mass index %d larger then length of previously read ljtypC %d"%(ind,len(parmC.ljtypC))
ljtyp_i = parmC.ljtypC[ljtyp_cnt]
ljtyp_i.setmass(mass_i)
else:
ljtyp_i = ljtype(ptype1)
ljtyp_i.setmass(mass_i)
parmC.ljtypC.put(ljtyp_i)
# Turn of mass read
if(cnt_Masses == n_atypes ):
read_Masses = 0
if( read_Pair and len(col) >= 3 ):
cnt_Pair += 1
ind = int(col[0]) - 1
ATYPE_EP[ind] = float(col[1])
ATYPE_SIG[ind] = float(col[2])
epsilon = float(col[1])
sigma = float(col[2])
ljtyp_ind = int(col[0])
ljtyp_i = parmC.ljtypC[ljtyp_ind]
ljtyp_i.setparam(epsilon,sigma)
# Turn pair parameter read off
if(cnt_Pair >= n_atypes ):
read_Pair = 0
if( read_Bond_coeff and len(col) >= 3 ):
cnt_Bond_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
b_ind = int( col[0]) - 1
if( b_ind > n_btypes ):
error_line = " Error in data file index of bond parameter exceeds number of bond parameters specified with bond types "
sys.exit(error_line)
BTYPE_REF[b_ind][0] = "??"
BTYPE_REF[b_ind][1] = "??"
BONDTYPE_K[b_ind] = float(col[1])
BONDTYPE_R0[b_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
lmpindx = int( col[0])
kb = float(col[1])
r0 = float(col[2])
btype = "harmonic"
g_type = 1
if( btyp_update ):
btyp_cnt = b_ind + 1
btyp_i = parmC.btypC[btyp_cnt]
btyp_i.setharmonic(r0,kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
else:
btyp_i = bondtype(ptype1,ptype2,btype)
btyp_i.setharmonic(r0,kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
parmC.btypC.put(btyp_i)
if( cnt_Bond_coeff >= n_btypes ):
read_Bond_coeff = 0
if( read_Angle_coeff and len(col) >= 3 ):
cnt_Angle_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
a_ind = int( col[0]) - 1
if( a_ind > n_angtypes ):
print sys.exit(" Error in data file index of angle parameter exceeds number of angle parameters specified with angle types ")
ANGTYPE_REF[a_ind][0] = "??"
ANGTYPE_REF[a_ind][1] = "??"
ANGTYPE_REF[a_ind][2] = "??"
ANGLETYPE_K[a_ind] = float(col[1])
ANGLETYPE_R0[a_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
lmpindx = int( col[0])
theta0 = float( col[2] ) # degrees
kb = float( col[1] )
atype = "harmonic"
gfunc_type = 1
if( atyp_update ):
atyp_cnt = a_ind + 1
atyp_i = parmC.atypC[atyp_cnt]
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0,kb)
else:
atyp_i = angletype(ptype1,ptype2,ptype3,atype)
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0,kb)
parmC.atypC.put(atyp_i)
if( cnt_Angle_coeff >= n_angtypes ):
read_Angle_coeff = 0
if( read_Dihedral_coeff and len(col) >= 3 ):
cnt_Dihedral_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
d_ind = int( col[0]) - 1
if( debug): print " reading dih type ",d_ind," cnt ",cnt_Dihedral_coeff," of ",n_dtypes
if( d_ind > n_dtypes ):
error_line = " Error in data file index of dihedral parameter %d exceeds number of dihedral parameters %d "%(d_ind , n_dtypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
DTYPE_REF[d_ind][0] = "??"
DTYPE_REF[d_ind][1] = "??"
DTYPE_REF[d_ind][2] = "??"
DTYPE_REF[d_ind][3] = "??"
# Assume OPLS dihedral type
DIHTYPE_F[d_ind] = 3
DIHTYPE_C[d_ind][0] = float(col[1])
DIHTYPE_C[d_ind][1] = float(col[2])
DIHTYPE_C[d_ind][2] = float(col[3])
DIHTYPE_C[d_ind][3] = float(col[4])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
gfunc_type = 3
dtype = "opls"
lmpindx = int( col[0] )
k1 = float( col[1] )
k2 = float( col[2] )
k3 = float( col[3] )
k4 = float( col[4] )
if( dtyp_update ):
dtyp_cnt = d_ind + 1
dtyp_i = parmC.dtypC[dtyp_cnt]
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1,k2,k3,k4)
else:
dtyp_i = dihtype(ptype1,ptype2,ptype3,ptype4,dtype)
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1,k2,k3,k4)
parmC.dtypC.put(dtyp_i)
if( cnt_Dihedral_coeff >= n_dtypes ):
read_Dihedral_coeff = 0
if( read_Improper_coeff and len(col) >= 3 ):
cnt_Improper_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
imp_ind = int( col[0]) - 1
if( debug): print " reading imp dih type ",imp_ind," cnt ",cnt_Improper_coeff," of ",n_imptypes
if( imp_ind > n_imptypes ):
error_line = " Error in data file index of improper parameter %d exceeds number of improper parameters %d "%(imp_ind , n_imptypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
IMPTYPE_REF[imp_ind][0] = "??"
IMPTYPE_REF[imp_ind][1] = "??"
IMPTYPE_REF[imp_ind][2] = "??"
IMPTYPE_REF[imp_ind][3] = "??"
# Assume OPLS dihedral type
IMPTYPE_F[imp_ind] = 2
KE = float(col[1])
Eo = float(col[2])
IMPTYPE_E0[imp_ind] = Eo
IMPTYPE_K[imp_ind] = KE
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
g_indx = 2
dtype = "improper"
lmpindx = int( col[0] )
if( imptyp_update ):
imptyp_cnt = imp_ind + 1
imptyp_i = parmC.imptypC[imptyp_cnt]
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo,KE)
imptyp_i.set_lmpindx(lmpindx)
else:
imptyp_i = imptype(ptype1,ptype2,ptype3,ptype4,dtype)
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo,KE)
imptyp_i.set_lmpindx(lmpindx)
parmC.imptypC.put(imptyp_i)
if( cnt_Improper_coeff >= n_imptypes ):
read_Improper_coeff = 0
if( read_Atoms and len(col) >= 7 ):
cnt_Atoms += 1
ind = int( col[0]) - 1
if( ind > n_atoms ):
print sys.exit(" Error in data file index of atoms exceeds number of atoms specified with atoms ")
chain_i = int(col[1])
lmptype_i = int(col[2]) #- 1
indx = int(col[2]) - 1
q_i = float(col[3])
m_i = ATYPE_MASS[indx]
fftype_i = ATYPE_REF[indx]
el = pt.getelementWithMass(m_i)
if( el.symbol == "VS" ):
el.symbol = ATYPE_l[atom_indx].strip()
fftype_i = "VS"
m_i = 0.0
# HACK !!
if( ATYPE_MASS[indx] == 9.0 ):
el.symbol = "LP"
fftype_i = "LP"
m_i = 0.0
r_i = [ float(col[4]),float(col[5]),float(col[6])]
type_i = str(lmptype_i)
#tagsD = {"chain":chain_i,"symbol":el.symbol,"number":el.number,"mass":el.mass,"cov_radii":el.cov_radii,"vdw_radii":el.vdw_radii}
#if( pt_overwrite ):
pt_i = strucC.ptclC[ind+1]
pt_i.position = r_i
update_coord = True
if( not update_coord ):
pt_i.type = el.symbol
pt_i.charge = q_i
pt_i.mass = m_i
add_dict = pt_i.tagsDict
# Set properties read in data file
if( set_chain_numbers ): add_dict["chain"] = chain_i
add_dict["symbol"] = el.symbol
add_dict["number"] = el.number
add_dict["mass"] = el.mass
add_dict["cov_radii"] = el.cov_radii
add_dict["vdw_radii"] = el.vdw_radii
add_dict["lmptype"] = lmptype_i
add_dict["fftype"] = fftype_i
#
add_dict["ffmass"] = ATYPE_MASS[indx]
add_dict["residue"] = chain_i
add_dict["qgroup"] = chain_i
add_dict["resname"] = "MOLR"
add_dict["ring"] = 0
add_dict["label"] = add_dict["symbol"]
pt_i.setTagsDict(add_dict)
if( cnt_Atoms >= n_atoms ):
read_Atoms = 0
if(read_Bonds and len(col) >= 4 ):
cnt_Bonds += 1
ind = int( col[0]) - 1
if( ind > n_bonds ):
print sys.exit(" Error in data file index of bonds exceeds number of bonds specified with bonds ")
BTYPE_IND[ind] = int(col[1] ) - 1
BONDS[ind] = [int(col[2]) - 1 , int(col[3]) - 1 ]
i_o = int(col[2])
j_o = int(col[3])
if( bonds_overwrite ):
bondObj = strucC.bondC[cnt_Bonds]
bondObj.pgid1 = i_o
bondObj.pgid2 = j_o
bondObj.set_lmpindx(int(col[1] ))
else:
bondObj = Bond( i_o, j_o )
bondObj.set_lmpindx(int(col[1] ))
strucC.bondC.put(bondObj)
if( cnt_Bonds >= n_bonds ):
read_Bonds = 0
if(read_Angles and len(col) >= 5 ):
cnt_Angles += 1
ind = int( col[0]) - 1
ANGTYPE_IND[ind] = int(col[1] ) - 1
ANGLES[ind] = [int(col[2]) - 1, int(col[3]) - 1, int(col[4]) - 1 ]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
if( cnt_Angles >= n_angles ):
read_Angles = 0
if( angles_overwrite ):
angleObj = strucC.angleC[cnt_Angles]
angleObj.pgid1 = k_o
angleObj.pgid2 = i_o
angleObj.pgid3 = j_o
angleObj.set_lmpindx(int(col[1] ))
else:
angleObj = Angle( k_o,i_o, j_o )
angleObj.set_lmpindx(int(col[1] ))
strucC.angleC.put(angleObj)
if(read_Dihedrals and len(col) >= 6 ):
cnt_Dihedrals += 1
ind = int( col[0]) - 1
DTYPE_IND[ind] = int(col[1] ) - 1
DIH[ind] = [int(col[2]) - 1,int(col[3]) - 1, int(col[4]) - 1,int(col[5]) - 1]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if( dih_overwrite ):
dObj = strucC.dihC[cnt_Dihedrals]
dObj.pgid1 = k_o
dObj.pgid2 = i_o
dObj.pgid3 = j_o
dObj.pgid4 = l_o
dObj.set_lmpindx(int(col[1] ))
else:
dObj = Dihedral( k_o,i_o, j_o,l_o )
dObj.set_lmpindx(int(col[1] ))
strucC.dihC.put(dObj)
if( cnt_Dihedrals >= n_dihedrals ):
read_Dihedrals = 0
if(read_Impropers and len(col) >= 2 ):
cnt_Impropers += 1
ind = int( col[0]) - 1
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if( imp_overwrite ):
impObj = strucC.impC[cnt_Impropers]
impObj.pgid1 = k_o
impObj.pgid2 = i_o
impObj.pgid3 = j_o
impObj.pgid4 = l_o
impObj.set_lmpindx(int(col[1] ))
impObj.set_type("improper")
else:
impObj = Improper( k_o,i_o, j_o,l_o )
impObj.set_lmpindx(int(col[1] ))
impObj.set_type("improper")
strucC.impC.put(impObj)
if( cnt_Impropers >= n_impropers ):
read_Impropers = 0
if ( len(col) >= 1 ):
if( col[0] == "Masses" ):
read_Masses = 1
cnt_Masses = 0
if( col[0] == "Atoms" ):
read_Atoms = 1
cnt_Atoms = 0
if( col[0] == "Bonds" ):
read_Bonds = 1
cnt_Bonds = 0
if( col[0] == "Angles" ):
read_Angles = 1
cnt_Angles = 0
if( col[0] == "Dihedrals" ):
read_Dihedrals = 1
cnt_Dihedrals = 0
if( col[0] == "Impropers" ):
read_Impropers = 1
cnt_Impropers = 0
if ( len(col) >= 2 ):
if( col[0] == "Pair" and col[1] == "Coeffs" ):
read_Pair = 1
cnt_Pair = 0
if( col[0] == "Bond" and col[1] == "Coeffs" ):
read_Bond_coeff = 1
cnt_Bond_coeff = 0
if( col[0] == "Angle" and col[1] == "Coeffs" ):
read_Angle_coeff = 1
cnt_Angle_coeff = 0
if( col[0] == "Dihedral" and col[1] == "Coeffs" ):
read_Dihedral_coeff = 1
cnt_Dihedral_coeff = 0
if( col[0] == "Improper" and col[1] == "Coeffs" ):
read_Improper_coeff = 1
cnt_Improper_coeff = 0
# cnt_Bonds += 1
# ind = int( col[0]) - 1
# BTYPE_IND[ind] = int(col[1] ) - 1
# BONDS[ind][0] = int(col[2])
# if( cnt_Bonds >= n_atoms ):
# read_Bonds = 0
#
#
if( ljtyp_update ):
if( ljtyp_cnt != len(parmC.ljtypC) ):
print " Number of LJ types read in %d does not match previously read %d "%(ljtyp_cnt,len(parmC.ljtypC))
if( debug):
for ind in range(len(ATYPE_MASS)):
print ind+1,ATYPE_MASS[ind]
for ind in range(len(ATYPE_EP)):
print ind+1,ATYPE_EP[ind],ATYPE_SIG[ind]
for ind in range(n_btypes):
print ind+1,BONDTYPE_R0[ind],BONDTYPE_K[ind]
for ind in range(n_angtypes):
print ind+1,ANGLETYPE_R0[ind],ANGLETYPE_K[ind]
for ind in range(n_dtypes):
print ind+1,DIHTYPE_C[ind]
debug =0
if( debug):
for ind in range(len(BONDS)):
print ind+1,BONDS[ind]
if(debug):
sys.exit("debug 1 ")
#
#
return (strucC,parmC)
def main():
"""
This test shows compressing IDs when structureContainer has angles included
"""
p1 = Particle([1.1, 1.1, 1.1], "Si", 2.0, 1.23)
p2 = Particle([2.2, 2.2, 2.2], "Si", 1.0, 2.34)
p3 = Particle([3.3, 3.3, 3.3], "Si", 1.0, 2.34)
p4 = Particle([0.0, 0.0, 0.0], "Si", 1.0, 2.34)
#
p5 = Particle([4.4, 4.4, 4.4], "C", 1.0, 2.34) # 1
p6 = Particle([5.5, 5.5, 5.5], "C", 1.0, 2.34) # 2
p7 = Particle([6.6, 6.6, 6.6], "C", 1.0, 2.34) # 3
b1 = Bond(1, 3, 1.11, "hooke")
b2 = Bond(3, 4, 2.22, "hooke")
#
b3 = Bond(1, 2, 3.33, "hooke")
b4 = Bond(2, 3, 4.44, "hooke")
a1 = Angle(1, 3, 4, 1.11, "harmonic")
#
a2 = Angle(1, 2, 3, 2.22, "harmonic")
atoms1 = ParticleContainer()
atoms2 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
atoms1.put(p4)
#
atoms2.put(p5)
atoms2.put(p6)
atoms2.put(p7)
del atoms1[2] # remove 2nd particle so ID's are non-consecutive
bonds1 = BondContainer()
bonds2 = BondContainer()
bonds1.put(b1)
bonds1.put(b2)
bonds2.put(b3)
bonds2.put(b4)
angles1 = AngleContainer()
angles2 = AngleContainer()
angles1.put(a1)
angles2.put(a2)
polymer1 = StructureContainer(atoms1, bonds1, angles1)
polymer2 = StructureContainer(atoms2, bonds2, angles2)
del p1, p2, p3, p4, p5, p6, b1, b2, b3, b4, a1, a2
del atoms1, atoms2, bonds1, bonds2, angles1, angles2
print "\n Cleaning memory for initial objects \n"
print "-------------------- Initial structures --------------------"
print "polymer1 = ", polymer1
print "polymer2 = ", polymer2
print " "
print "-------------- After adding (polymer2 += polymer1) ----------------"
polymer2 += polymer1
print "polymer2 = ", polymer2
polymer2.compressPtclIDs()
print "-------------------- After compressing --------------------"
print "polymer2 = ", polymer2
import stellariumConnect, datetime, math
from angles import Angle
from twoStarCalibrate import twoStarCalibrate
import numpy as np
from configParser import calibrationParser
stel1 = [Angle(r=1.6666*math.pi),Angle(r=math.pi/4)]
stel2 = [Angle(r=-math.pi/1.1),Angle(r=math.pi/52)]
tel1 = [Angle(r= -2.084132566391469),Angle(r= 0.785398163397448)]
tel2 = [Angle(r= 2.390466410049688),Angle(r= 0.060415243338265)]
TSC = twoStarCalibrate()
TSC.addStar(tel1, stel1)
TSC.addStar(tel2, stel2)
R = TSC.twoStarRotationMatrix()
R1 = TSC.oneStarRotaionMatrix()
TSC.addRotationMatrix(R)
[Az2,Alt2] = TSC.correct(-3.036725575684632, 0.300000000000000)
calP = calibrationParser("instrumentCalibration.xml")
calP.setAzAltCorrection(R)
Rp = calP.getAzAltCorrection()
print Rp
print R
print [Az2,Alt2]
def game_loop(self):
global x, y, font, text, screen
def clear():
screen.fill(BLACK)
pygame.init()
x = gtk.gdk.screen_width()
y = gtk.gdk.screen_height() - 55
half_x = x / 2
half_y = y / 2
screen = pygame.display.get_surface()
angleDisplay = screen.subsurface(
(x * .18, y * .1, x - (2 * x * .18), y - (2 * y * .1)))
self.planetNear = Image(
PLANET_PREFIX + str(randint(0, PLANET_NUMBER - 1)) + PLANET_SUFFIX,
screen)
self.planetFar = Image(
PLANET_PREFIX + str(randint(0, PLANET_NUMBER - 1)) + PLANET_SUFFIX,
angleDisplay)
# This is what a clicked button will call. so handle an answer here
def saveAnswer(answer):
# fill with black to wipe the screen. Otherwise the answer labels stack on each other
# We wont need this when we are not outputting the answer.
if (angle.checkAnswer(answer)):
print('correct')
score.increment()
angle.setRandomAngle()
print self.planetNear.image
self.planetNear.originalImage = self.planetFar.originalImage
self.planetFar = Image(
PLANET_PREFIX + str(randint(0, PLANET_NUMBER - 1)) +
PLANET_SUFFIX, angleDisplay)
putPlanets(self.planetNear, self.planetFar)
else:
print('wrong')
loseGame('')
score.reset()
def startGame(msg):
global state
state = GAME
screen.fill(BLACK)
def loseGame(msg):
global state
state = OVER
clear()
def mainMenu(msg):
global state
state = MAIN
clear()
def putPlanets(near, far):
near.setSize(x * NEAR_SIZE, x * NEAR_SIZE)
near.move(half_x, half_y)
near.rect.center = near.rect.topleft
far.setSize(x * FAR_SIZE, x * FAR_SIZE)
far.move(angle.top[0], angle.top[1])
far.rect.center = far.rect.topleft
pygame.display.set_caption('Angles')
font = pygame.font.SysFont(None, 48)
smallFont = pygame.font.SysFont(None, 30)
clock = pygame.time.Clock()
scoreDisplay = screen.subsurface(
(x * SCORE_X, y * SCORE_Y, x - (x * SCORE_X), y - (y * SCORE_Y)))
angle = Angle(angleDisplay, 150, _ypercent=.3)
tux = Image(TUX_IMAGE, screen)
tux.move(half_x, half_y)
tux.rect.midbottom = tux.rect.topleft
putPlanets(self.planetNear, self.planetFar)
score = ScoreTicker(x, y, scoreDisplay)
but_half = (x * BUT_W / 2)
rightBut = Button("Right", x * B1_X, y * B1_Y, x * BUT_W, y * BUT_H,
screen, saveAnswer)
acuteBut = Button("Acute", x * B2_X, y * B2_Y, x * BUT_W, y * BUT_H,
screen, saveAnswer)
obtBut = Button("Obtuse", x * B3_X, y * B3_Y, x * BUT_W, y * BUT_H,
screen, saveAnswer)
#Game State Stuff
startBut = Button("Start", (x * B4_X) - but_half, y * B4_Y, x * BUT_W,
y * BUT_H, screen, startGame)
mainBut = Button("Menu", (x * B5_X) - but_half, y * B5_Y, x * BUT_W,
y * BUT_H, screen, mainMenu)
restartBut = Button("Restart", (x * B6_X) - but_half, y * B6_Y,
x * BUT_W, y * BUT_H, screen, startGame)
mainText = font.render("Tux Explorer", True, WHITE, BLACK)
mainHalfWidth = mainText.get_width() / 2
main_xpos = half_x - mainHalfWidth
main_ypos = MAIN_Y * y
helpText1 = smallFont.render(
"Tux is lost! Help him navigate through space.", True, WHITE,
BLACK)
help1_xpos = half_x - (helpText1.get_width() / 2)
help1_ypos = HELP1_Y * y
helpText2 = smallFont.render(
"Tell him if his angle to the next planet is acute, obtuse, or right.",
True, WHITE, BLACK)
help2_xpos = half_x - (helpText2.get_width() / 2)
help2_ypos = HELP2_Y * y
overText = font.render("Game Over!", True, WHITE, BLACK)
overHalfWidth = overText.get_width() / 2
over_xpos = half_x - overHalfWidth
over_ypos = OVER_Y * y
global state
state = MAIN
while 1:
while gtk.events_pending():
gtk.main_iteration()
clicked = False
for event in pygame.event.get():
if event.type == pygame.QUIT:
# Change "Juego Finalizado" to change the exit message (log)
score.saveScore()
exit("Game Finalized")
elif event.type == pygame.VIDEORESIZE:
pygame.display.set_mode(event.size, pygame.RESIZABLE)
elif event.type == pygame.MOUSEBUTTONUP:
clicked = True
if state == MAIN:
screen.blit(mainText, (main_xpos, main_ypos))
screen.blit(helpText1, (help1_xpos, help1_ypos))
screen.blit(helpText2, (help2_xpos, help2_ypos))
startBut.draw(clicked)
elif state == GAME:
obtBut.draw(clicked)
acuteBut.draw(clicked)
rightBut.draw(clicked)
score.draw()
angle.draw()
self.planetNear.draw()
tux.draw()
self.planetFar.draw()
else:
screen.fill(BLACK)
screen.blit(overText, (over_xpos, over_ypos))
mainBut.draw(clicked)
restartBut.draw(clicked)
pygame.display.flip()
# Try to stay at 30 FPS
clock.tick(30)
def loadCoordsFile(fileName, clmsSpecification, dlm=','):
"""
This function loads a file that contains points along with their
respective coordinates. A sample row of this file may have the
following format:
p4,4478329.405,1921444.508,4101378.606, 41.464, 42.651
where each delimited value corresponds to:
id, E/X/lat, N/Y/lon, U/Z/h, geoidHeight, GMHeight respectively.
and
id: point id
ENU: map coordinates
XYZ: ECEF coordinates
latlonh: geodetic coordinates
geoidHeight: geoid undulation, i.e. geoidHeight = h - U
GMHeight: geoid undulation coming from a geopotential model as EGM08
* All coordinates values expressed in meters, except lat, lon where their
values could be radians or degrees in the following formats:
decimal degrees-dd, e.g. -0.1927322, degrees:minutes-dm, e.g. 11:2.3474,
degrees:minutes:seconds-dms, e.g. -0:59:59.0001123
Arguments
fileName: string that specifies the name of file to be loaded
clmsSpecification: list of strings, that specifies what each column
represent and in what order the columns are layout.
possible list any subset of:
['id', 'X', 'Y', 'Z', lat-r/dd/dm/dms,
lon-r/dd/dm/dms, h, E, N, U, 'geoidHeight',
'GMHeight']
e.g. ['id', 'X', 'Y', 'Z'] or
['id', 'Z', 'Y', 'X', 'geoidHeight']
lat-r/dd/dm/dms means that it could be
lat-r or lat-dd or lat-dm or lat-dms. The same
holds for lon-r/dd/dm/dms
dlm: one character string that specifies file's delimiter
e.g. ' ', ',', '\t'
Returns
any possible subset (concerning keys) of the follwoing dictionary:
{'id': [strings], 'X': [numbers], 'Y': [numbers], 'Z': [numbers],
'lat-r/dd/dm/dms': [numbers/strings],
'lon-r/dd/dm/dms': [numbers/strings], 'h': [numbers], 'E': [numbers],
'N': [numbers], 'U': [numbers]
'geoidHeight': [numbers], 'GMHeight': [numbers]}
"""
if len(set(clmsSpecification)) != len(clmsSpecification):
raise Exception("Your columns specification contain duplicates")
allClms = {'id', 'X', 'Y', 'Z', 'lat-r', 'lon-r', 'lat-dd', 'lon-dd',
'lat-dm', 'lon-dm', 'lat-dms', 'lon-dms', 'h', 'E', 'N', 'U',
'geoidHeight', 'GMHeight'}
if not set(clmsSpecification).issubset(allClms):
raise Exception("Define columns specification properly")
with open(fileName) as fObj:
readCSV = reader(fObj, delimiter=dlm)
data = defaultdict(list)
for line in readCSV:
if line:
for key, value in zip(clmsSpecification, line):
data[key].append(value.strip())
latlonInDeg = ['lat-dd', 'lon-dd', 'lat-dm', 'lon-dm',
'lat-dms', 'lon-dms']
for key in set(data.keys()) - {'id'}:
# if key not in latlonInDeg:
# data[key] = [float(x) for x in data[key]]
if key in ['lat-r', 'lon-r']:
data[key] = [Angle(float(x)) for x in data[key]]
elif key in latlonInDeg:
data[key] = [Angle(x) for x in data[key]]
else:
data[key] = [float(x) for x in data[key]]
return data
def read_lmpdata(strucC, parmC, data_file):
"""
Read Lammps data file
Arguments:
strucC (StructureContainer)
parmC (ParameterContainer)
data_file (str) data file
ReturnS:
strucC (StructureContainer)
parmC (ParameterContainer)
"""
debug = 0
verbose = True
set_chain_numbers = True
if (not set_chain_numbers):
print " Warning not reading in chain numbers!!! "
# Load periodic table
pt = periodictable()
F = open(data_file, 'r')
lines = F.readlines()
F.close()
#
# Read in data header with number of parameters
#
for line in lines:
col = line.split()
if (len(col) >= 2):
# Read in number of each topolgical component
if (col[1] == "atoms"):
n_atoms = int(col[0])
elif (col[1] == "bonds"):
n_bonds = int(col[0])
elif (col[1] == "angles"):
n_angles = int(col[0])
elif (col[1] == "dihedrals"):
n_dihedrals = int(col[0])
elif (col[1] == "impropers"):
n_impropers = int(col[0])
if (len(col) >= 3):
# Read in number of each parameter type
if (col[1] == "atom" and col[2] == "types"):
n_atypes = int(col[0])
elif (col[1] == "bond" and col[2] == "types"):
n_btypes = int(col[0])
elif (col[1] == "angle" and col[2] == "types"):
n_angtypes = int(col[0])
elif (col[1] == "dihedral" and col[2] == "types"):
n_dtypes = int(col[0])
elif (col[1] == "improper" and col[2] == "types"):
n_imptypes = int(col[0])
# Read in box size
if (len(col) >= 4):
if (col[2] == "xlo" and col[3] == "xhi"):
strucC.latvec[0][0] = float(col[1]) - float(col[0])
if (col[2] == "ylo" and col[3] == "yhi"):
strucC.latvec[1][1] = float(col[1]) - float(col[0])
if (col[2] == "zlo" and col[3] == "zhi"):
strucC.latvec[2][2] = float(col[1]) - float(col[0])
# Prind debug
if (verbose):
print " atoms ", n_atoms
print " n_bonds ", n_bonds
print " n_angles ", n_angles
print " n_dihedrals ", n_dihedrals
print " n_impropers ", n_impropers
print ""
print "n_atom_types", n_atypes
print "n_bond_types", n_btypes
print "n_angle_types", n_angtypes
print "n_dihedral_types", n_dtypes
print "n_imp_dihedral_types", n_imptypes
# Check to see if a previous read has occured
pt_overwrite = False
if (len(strucC.ptclC) > 0):
pt_overwrite = True
# Check of conistent number of atoms
if (pt_overwrite):
if (len(strucC.ptclC) != n_atoms):
print " %d atoms in passed structure " % (len(strucC.ptclC))
print " %d atoms in data file " % (n_atoms)
sys.exit(" Inconsistent number of atoms ")
else:
#
# Initialize particle container
#
for pid_i in range(n_atoms):
pt_i = Particle()
strucC.ptclC.put(pt_i)
bonds_overwrite = False
if (len(strucC.bondC) > 0):
bonds_overwrite = True
if (len(strucC.bondC) != n_bonds):
print " %d bonds in passed structure " % (len(strucC.bondC))
print " %d bonds in data file " % (n_bonds)
sys.exit(" Inconsistent number of bonds ")
angles_overwrite = False
if (len(strucC.angleC) > 0):
angles_overwrite = True
if (len(strucC.angleC) != n_angles):
print " %d angles in passed structure " % (len(strucC.angleC))
print " %d angles in data file " % (n_angles)
sys.exit(" Inconsistent number of angles ")
dih_overwrite = False
if (len(strucC.dihC) > 0):
dih_overwrite = True
if (len(strucC.dihC) != n_dihedrals):
print " %d dihedrals in passed structure " % (len(strucC.dihC))
print " %d dihedrals in data file " % (n_dihedrals)
sys.exit(" Inconsistent number of dihedrals ")
imp_overwrite = False
if (len(strucC.impC) > 0):
imp_overwrite = True
if (len(strucC.impC) != n_impropers):
print " %d impropers in passed structure " % (len(strucC.impC))
print " %d impropers in data file " % (n_impropers)
sys.exit(" Inconsistent number of impropers ")
#
# Intialize
# - read in boolean to off
#
read_Masses = 0
read_Pair = 0
read_Bond_coeff = 0
read_Angle_coeff = 0
read_Dihedral_coeff = 0
read_Improper_coeff = 0
read_Atoms = 0
read_Bonds = 0
read_Angles = 0
read_Dihedrals = 0
read_Impropers = 0
# - lists as indecise can be out of order in data file
ATYPE_REF = n_atypes * [""]
ATYPE_MASS = np.zeros(n_atypes)
ATYPE_EP = np.zeros(n_atypes)
ATYPE_SIG = np.zeros(n_atypes)
BTYPE_REF = n_btypes * [2 * [""]]
BONDTYPE_R0 = np.zeros(n_btypes)
BONDTYPE_K = np.zeros(n_btypes)
ANGTYPE_REF = n_angtypes * [3 * [""]]
ANGLETYPE_R0 = np.zeros(n_angtypes)
ANGLETYPE_K = np.zeros(n_angtypes)
DTYPE_REF = n_dtypes * [4 * [""]]
DIHTYPE_C = np.zeros((n_dtypes, 4))
DIHTYPE_F = np.zeros(n_dtypes)
DIHTYPE_K = np.zeros(n_dtypes)
DIHTYPE_PN = np.zeros(n_dtypes)
DIHTYPE_PHASE = np.zeros(n_dtypes)
IMPTYPE_REF = n_imptypes * [4 * [""]]
IMPTYPE_F = np.zeros(n_imptypes)
IMPTYPE_E0 = np.zeros(n_imptypes)
IMPTYPE_K = np.zeros(n_imptypes)
MOLNUMB = n_atoms * [0]
ATYPE_IND = n_atoms * [0]
CHARGES = np.zeros(n_atoms)
R = n_atoms * [np.zeros(3)]
ATYPE = n_atoms * [""]
BONDS = n_bonds * [[0, 0]]
BTYPE_IND = n_bonds * [0]
ANGLES = n_angles * [[0, 0, 0]]
ANGTYPE_IND = n_angles * [0]
DIH = n_dihedrals * [[0, 0, 0, 0]]
DTYPE_IND = n_dihedrals * [0]
#
# Check if values exist and need to be updated or don't and need to be created
#
ljtyp_update = False
ljtyp_cnt = 0
if (len(parmC.ljtypC) > 0):
print " LJ types will be updated "
ljtyp_update = True
btyp_update = False
btyp_cnt = 0
if (len(parmC.btypC) > 0):
print " Bond types will be updated "
btyp_update = True
atyp_update = False
atyp_cnt = 0
if (len(parmC.atypC) > 0):
print " Angle types will be updated "
atyp_update = True
dtyp_update = False
dtyp_cnt = 0
if (len(parmC.dtypC) > 0):
print " Dihedral types will be updated "
dtyp_update = True
imptyp_update = False
imptyp_cnt = 0
if (len(parmC.imptypC) > 0):
print " Improper dihedrals types will be updated "
imptyp_update = True
#
# Read in data parameters
#
for line in lines:
col = line.split()
if (read_Masses and len(col) >= 2):
cnt_Masses += 1
ind = int(col[0]) - 1
ATYPE_MASS[ind] = float(col[1])
if (len(col) >= 4):
ATYPE_REF[ind] = col[3]
ptype1 = col[3]
else:
ATYPE_REF[ind] = "??"
ptype1 = "??"
mass_i = float(col[1])
if (ljtyp_update):
ljtyp_cnt = ind + 1
if (ljtyp_cnt > len(parmC.ljtypC)):
print "Mass index %d larger then length of previously read ljtypC %d" % (
ind, len(parmC.ljtypC))
ljtyp_i = parmC.ljtypC[ljtyp_cnt]
ljtyp_i.setmass(mass_i)
else:
ljtyp_i = ljtype(ptype1)
ljtyp_i.setmass(mass_i)
parmC.ljtypC.put(ljtyp_i)
# Turn of mass read
if (cnt_Masses == n_atypes):
read_Masses = 0
if (read_Pair and len(col) >= 3):
cnt_Pair += 1
ind = int(col[0]) - 1
ATYPE_EP[ind] = float(col[1])
ATYPE_SIG[ind] = float(col[2])
epsilon = float(col[1])
sigma = float(col[2])
ljtyp_ind = int(col[0])
ljtyp_i = parmC.ljtypC[ljtyp_ind]
ljtyp_i.setparam(epsilon, sigma)
# Turn pair parameter read off
if (cnt_Pair >= n_atypes):
read_Pair = 0
if (read_Bond_coeff and len(col) >= 3):
cnt_Bond_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
b_ind = int(col[0]) - 1
if (b_ind > n_btypes):
error_line = " Error in data file index of bond parameter exceeds number of bond parameters specified with bond types "
sys.exit(error_line)
BTYPE_REF[b_ind][0] = "??"
BTYPE_REF[b_ind][1] = "??"
BONDTYPE_K[b_ind] = float(col[1])
BONDTYPE_R0[b_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
lmpindx = int(col[0])
kb = float(col[1])
r0 = float(col[2])
btype = "harmonic"
g_type = 1
if (btyp_update):
btyp_cnt = b_ind + 1
btyp_i = parmC.btypC[btyp_cnt]
btyp_i.setharmonic(r0, kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
else:
btyp_i = bondtype(ptype1, ptype2, btype)
btyp_i.setharmonic(r0, kb)
btyp_i.set_g_indx(g_type)
btyp_i.set_lmpindx(lmpindx)
parmC.btypC.put(btyp_i)
if (cnt_Bond_coeff >= n_btypes):
read_Bond_coeff = 0
if (read_Angle_coeff and len(col) >= 3):
cnt_Angle_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
a_ind = int(col[0]) - 1
if (a_ind > n_angtypes):
print sys.exit(
" Error in data file index of angle parameter exceeds number of angle parameters specified with angle types "
)
ANGTYPE_REF[a_ind][0] = "??"
ANGTYPE_REF[a_ind][1] = "??"
ANGTYPE_REF[a_ind][2] = "??"
ANGLETYPE_K[a_ind] = float(col[1])
ANGLETYPE_R0[a_ind] = float(col[2])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
lmpindx = int(col[0])
theta0 = float(col[2]) # degrees
kb = float(col[1])
atype = "harmonic"
gfunc_type = 1
if (atyp_update):
atyp_cnt = a_ind + 1
atyp_i = parmC.atypC[atyp_cnt]
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0, kb)
else:
atyp_i = angletype(ptype1, ptype2, ptype3, atype)
atyp_i.set_g_indx(gfunc_type)
atyp_i.set_lmpindx(lmpindx)
atyp_i.setharmonic(theta0, kb)
parmC.atypC.put(atyp_i)
if (cnt_Angle_coeff >= n_angtypes):
read_Angle_coeff = 0
if (read_Dihedral_coeff and len(col) >= 3):
cnt_Dihedral_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
d_ind = int(col[0]) - 1
if (debug):
print " reading dih type ", d_ind, " cnt ", cnt_Dihedral_coeff, " of ", n_dtypes
if (d_ind > n_dtypes):
error_line = " Error in data file index of dihedral parameter %d exceeds number of dihedral parameters %d " % (
d_ind, n_dtypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
DTYPE_REF[d_ind][0] = "??"
DTYPE_REF[d_ind][1] = "??"
DTYPE_REF[d_ind][2] = "??"
DTYPE_REF[d_ind][3] = "??"
# Assume OPLS dihedral type
DIHTYPE_F[d_ind] = 3
DIHTYPE_C[d_ind][0] = float(col[1])
DIHTYPE_C[d_ind][1] = float(col[2])
DIHTYPE_C[d_ind][2] = float(col[3])
DIHTYPE_C[d_ind][3] = float(col[4])
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
gfunc_type = 3
dtype = "opls"
lmpindx = int(col[0])
k1 = float(col[1])
k2 = float(col[2])
k3 = float(col[3])
k4 = float(col[4])
if (dtyp_update):
dtyp_cnt = d_ind + 1
dtyp_i = parmC.dtypC[dtyp_cnt]
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1, k2, k3, k4)
else:
dtyp_i = dihtype(ptype1, ptype2, ptype3, ptype4, dtype)
dtyp_i.set_g_indx(gfunc_type)
dtyp_i.set_lmpindx(lmpindx)
dtyp_i.setopls(k1, k2, k3, k4)
parmC.dtypC.put(dtyp_i)
if (cnt_Dihedral_coeff >= n_dtypes):
read_Dihedral_coeff = 0
if (read_Improper_coeff and len(col) >= 3):
cnt_Improper_coeff += 1
#AT_i = int(col[0])
#AT_j = int(col[1])
imp_ind = int(col[0]) - 1
if (debug):
print " reading imp dih type ", imp_ind, " cnt ", cnt_Improper_coeff, " of ", n_imptypes
if (imp_ind > n_imptypes):
error_line = " Error in data file index of improper parameter %d exceeds number of improper parameters %d " % (
imp_ind, n_imptypes)
error_line += " specified with dihedral types "
print sys.exit(error_line)
IMPTYPE_REF[imp_ind][0] = "??"
IMPTYPE_REF[imp_ind][1] = "??"
IMPTYPE_REF[imp_ind][2] = "??"
IMPTYPE_REF[imp_ind][3] = "??"
# Assume OPLS dihedral type
IMPTYPE_F[imp_ind] = 2
KE = float(col[1])
Eo = float(col[2])
IMPTYPE_E0[imp_ind] = Eo
IMPTYPE_K[imp_ind] = KE
ptype1 = "??"
ptype2 = "??"
ptype3 = "??"
ptype4 = "??"
# Set parameters according to type
g_indx = 2
dtype = "improper"
lmpindx = int(col[0])
if (imptyp_update):
imptyp_cnt = imp_ind + 1
imptyp_i = parmC.imptypC[imptyp_cnt]
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo, KE)
imptyp_i.set_lmpindx(lmpindx)
else:
imptyp_i = imptype(ptype1, ptype2, ptype3, ptype4, dtype)
imptyp_i.set_g_indx(g_indx)
imptyp_i.setimp(Eo, KE)
imptyp_i.set_lmpindx(lmpindx)
parmC.imptypC.put(imptyp_i)
if (cnt_Improper_coeff >= n_imptypes):
read_Improper_coeff = 0
if (read_Atoms and len(col) >= 7):
cnt_Atoms += 1
ind = int(col[0]) - 1
if (ind > n_atoms):
print sys.exit(
" Error in data file index of atoms exceeds number of atoms specified with atoms "
)
chain_i = int(col[1])
lmptype_i = int(col[2]) #- 1
indx = int(col[2]) - 1
q_i = float(col[3])
m_i = ATYPE_MASS[indx]
fftype_i = ATYPE_REF[indx]
el = pt.getelementWithMass(m_i)
if (el.symbol == "VS"):
el.symbol = ATYPE_l[atom_indx].strip()
fftype_i = "VS"
m_i = 0.0
# HACK !!
if (ATYPE_MASS[indx] == 9.0):
el.symbol = "LP"
fftype_i = "LP"
m_i = 0.0
r_i = [float(col[4]), float(col[5]), float(col[6])]
type_i = str(lmptype_i)
#tagsD = {"chain":chain_i,"symbol":el.symbol,"number":el.number,"mass":el.mass,"cov_radii":el.cov_radii,"vdw_radii":el.vdw_radii}
#if( pt_overwrite ):
pt_i = strucC.ptclC[ind + 1]
pt_i.position = r_i
pt_i.charge = q_i
pt_i.mass = m_i
add_dict = pt_i.tagsDict
# Set properties read in data file
if (set_chain_numbers): add_dict["chain"] = chain_i
add_dict["symbol"] = el.symbol
add_dict["number"] = el.number
add_dict["mass"] = el.mass
add_dict["cov_radii"] = el.cov_radii
add_dict["vdw_radii"] = el.vdw_radii
add_dict["lmptype"] = lmptype_i
add_dict["fftype"] = fftype_i
#
add_dict["ffmass"] = ATYPE_MASS[indx]
pt_i.setTagsDict(add_dict)
if (cnt_Atoms >= n_atoms):
read_Atoms = 0
if (read_Bonds and len(col) >= 4):
cnt_Bonds += 1
ind = int(col[0]) - 1
if (ind > n_bonds):
print sys.exit(
" Error in data file index of bonds exceeds number of bonds specified with bonds "
)
BTYPE_IND[ind] = int(col[1]) - 1
BONDS[ind] = [int(col[2]) - 1, int(col[3]) - 1]
i_o = int(col[2])
j_o = int(col[3])
if (bonds_overwrite):
bondObj = strucC.bondC[cnt_Bonds]
bondObj.pgid1 = i_o
bondObj.pgid2 = j_o
bondObj.set_lmpindx(int(col[1]))
else:
bondObj = Bond(i_o, j_o)
bondObj.set_lmpindx(int(col[1]))
strucC.bondC.put(bondObj)
if (cnt_Bonds >= n_bonds):
read_Bonds = 0
if (read_Angles and len(col) >= 5):
cnt_Angles += 1
ind = int(col[0]) - 1
ANGTYPE_IND[ind] = int(col[1]) - 1
ANGLES[ind] = [int(col[2]) - 1, int(col[3]) - 1, int(col[4]) - 1]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
if (cnt_Angles >= n_angles):
read_Angles = 0
if (angles_overwrite):
angleObj = strucC.angleC[cnt_Angles]
angleObj.pgid1 = k_o
angleObj.pgid2 = i_o
angleObj.pgid3 = j_o
angleObj.set_lmpindx(int(col[1]))
else:
angleObj = Angle(k_o, i_o, j_o)
angleObj.set_lmpindx(int(col[1]))
strucC.angleC.put(angleObj)
if (read_Dihedrals and len(col) >= 6):
cnt_Dihedrals += 1
ind = int(col[0]) - 1
DTYPE_IND[ind] = int(col[1]) - 1
DIH[ind] = [
int(col[2]) - 1,
int(col[3]) - 1,
int(col[4]) - 1,
int(col[5]) - 1
]
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if (dih_overwrite):
dObj = strucC.dihC[cnt_Dihedrals]
dObj.pgid1 = k_o
dObj.pgid2 = i_o
dObj.pgid3 = j_o
dObj.pgid4 = l_o
dObj.set_lmpindx(int(col[1]))
else:
dObj = Dihedral(k_o, i_o, j_o, l_o)
dObj.set_lmpindx(int(col[1]))
strucC.dihC.put(dObj)
if (cnt_Dihedrals >= n_dihedrals):
read_Dihedrals = 0
if (read_Impropers and len(col) >= 2):
cnt_Impropers += 1
ind = int(col[0]) - 1
k_o = int(col[2])
i_o = int(col[3])
j_o = int(col[4])
l_o = int(col[5])
if (imp_overwrite):
impObj = strucC.impC[cnt_Impropers]
impObj.pgid1 = k_o
impObj.pgid2 = i_o
impObj.pgid3 = j_o
impObj.pgid4 = l_o
impObj.set_lmpindx(int(col[1]))
impObj.set_type("improper")
else:
impObj = Improper(k_o, i_o, j_o, l_o)
impObj.set_lmpindx(int(col[1]))
impObj.set_type("improper")
strucC.impC.put(impObj)
if (cnt_Impropers >= n_impropers):
read_Impropers = 0
if (len(col) >= 1):
if (col[0] == "Masses"):
read_Masses = 1
cnt_Masses = 0
if (col[0] == "Atoms"):
read_Atoms = 1
cnt_Atoms = 0
if (col[0] == "Bonds"):
read_Bonds = 1
cnt_Bonds = 0
if (col[0] == "Angles"):
read_Angles = 1
cnt_Angles = 0
if (col[0] == "Dihedrals"):
read_Dihedrals = 1
cnt_Dihedrals = 0
if (col[0] == "Impropers"):
read_Impropers = 1
cnt_Impropers = 0
if (len(col) >= 2):
if (col[0] == "Pair" and col[1] == "Coeffs"):
read_Pair = 1
cnt_Pair = 0
if (col[0] == "Bond" and col[1] == "Coeffs"):
read_Bond_coeff = 1
cnt_Bond_coeff = 0
if (col[0] == "Angle" and col[1] == "Coeffs"):
read_Angle_coeff = 1
cnt_Angle_coeff = 0
if (col[0] == "Dihedral" and col[1] == "Coeffs"):
read_Dihedral_coeff = 1
cnt_Dihedral_coeff = 0
if (col[0] == "Improper" and col[1] == "Coeffs"):
read_Improper_coeff = 1
cnt_Improper_coeff = 0
# cnt_Bonds += 1
# ind = int( col[0]) - 1
# BTYPE_IND[ind] = int(col[1] ) - 1
# BONDS[ind][0] = int(col[2])
# if( cnt_Bonds >= n_atoms ):
# read_Bonds = 0
#
#
if (ljtyp_update):
if (ljtyp_cnt != len(parmC.ljtypC)):
print " Number of LJ types read in %d does not match previously read %d " % (
ljtyp_cnt, len(parmC.ljtypC))
if (debug):
for ind in range(len(ATYPE_MASS)):
print ind + 1, ATYPE_MASS[ind]
for ind in range(len(ATYPE_EP)):
print ind + 1, ATYPE_EP[ind], ATYPE_SIG[ind]
for ind in range(n_btypes):
print ind + 1, BONDTYPE_R0[ind], BONDTYPE_K[ind]
for ind in range(n_angtypes):
print ind + 1, ANGLETYPE_R0[ind], ANGLETYPE_K[ind]
for ind in range(n_dtypes):
print ind + 1, DIHTYPE_C[ind]
debug = 0
if (debug):
for ind in range(len(BONDS)):
print ind + 1, BONDS[ind]
if (debug):
sys.exit("debug 1 ")
#
#
return (strucC, parmC)
def main():
"""
This test shows structureContainer functionality with dihedrals included
"""
print "************************************************************************************"
print " This test shows structureContainer functionality with dihedrals included"
print "************************************************************************************ \n"
p1 = Particle([1.1, 1.1, 1.1], "Si", 2.0, 1.23)
p2 = Particle([2.2, 2.2, 2.2], "Si", 1.0, 2.34)
p3 = Particle([3.3, 3.3, 3.3], "Si", 1.0, 2.34)
p4 = Particle([4.4, 4.4, 4.4], "Si", 1.0, 2.34)
#
p5 = Particle([5.5, 5.5, 5.5], "C", 1.0, 2.34) # 1
p6 = Particle([6.6, 6.6, 6.6], "C", 1.0, 2.34) # 2
p7 = Particle([7.7, 7.7, 7.7], "C", 1.0, 2.34) # 3
p8 = Particle([8.8, 8.8, 8.8], "C", 1.0, 2.34) # 4
b1 = Bond(1, 2, 1.11, "hooke")
b2 = Bond(2, 3, 2.22, "hooke")
b3 = Bond(3, 4, 3.33, "hooke")
#
b4 = Bond(1, 2, 4.44, "hooke")
b5 = Bond(2, 3, 5.55, "hooke")
b6 = Bond(3, 4, 6.66, "hooke")
a1 = Angle(1, 2, 3, 1.11, "harmonic")
#
a2 = Angle(1, 2, 3, 2.22, "harmonic")
d1 = Dihedral(1, 2, 3, 4, 1.11, "stiff")
#
d2 = Dihedral(1, 2, 3, 4, 2.22, "stiff")
atoms1 = ParticleContainer()
atoms2 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
atoms1.put(p4)
#
atoms2.put(p5)
atoms2.put(p6)
atoms2.put(p7)
atoms2.put(p8)
bonds1 = BondContainer()
bonds2 = BondContainer()
bonds1.put(b1)
bonds1.put(b2)
bonds1.put(b3)
#
bonds2.put(b4)
bonds2.put(b5)
bonds2.put(b6)
angles1 = AngleContainer()
angles2 = AngleContainer()
angles1.put(a1)
angles2.put(a2)
dih1 = DihedralContainer()
dih2 = DihedralContainer()
dih1.put(d1)
dih2.put(d2)
polymer1 = StructureContainer(atoms1, bonds1, angles1, dih1)
polymer2 = StructureContainer(atoms2, bonds2, angles2, dih2)
del p1, p2, p3, p4, p5, p6, p7, p8
del b1, b2, b3, b4, b5, b6, a1, a2, d1, d2
del atoms1, atoms2, bonds1, bonds2, angles1, angles2, dih1, dih2
print "\n Cleaning memory for initial objects \n"
print "-------------------- Initial structures --------------------"
print "polymer1 = ", polymer1
print "polymer2 = ", polymer2
print " "
print "-------------- After adding (polymer1 += polymer2) ----------------"
polymer2 += polymer1
print "polymer2 = ", polymer2
def main():
"""
This test shows structureContainer functionality with angles included
"""
print "************************************************************************************"
print " This test shows structureContainer functionality with angles included"
print "************************************************************************************ \n"
p1 = Particle( [1.1, 1.1, 1.1], "Si", 2.0, 1.23)
p2 = Particle( [2.2, 2.2, 2.2], "Si", 1.0, 2.34)
p3 = Particle( [3.3, 3.3, 3.3], "Si", 1.0, 2.34)
#
p4 = Particle( [4.4, 4.4, 4.4], "C", 1.0, 2.34) # 1
p5 = Particle( [5.5, 5.5, 5.5], "C", 1.0, 2.34) # 2
p6 = Particle( [6.6, 6.6, 6.6], "C", 1.0, 2.34) # 3
b1 = Bond( 1, 2, 1.11, "hooke")
b2 = Bond( 2, 3, 2.22, "hooke")
#
b3 = Bond( 1, 2, 3.33, "hooke")
b4 = Bond( 2, 3, 4.44, "hooke")
a1 = Angle(1, 2, 3, 1.11, "harmonic")
#
a2 = Angle(1, 2, 3, 2.22, "harmonic")
atoms1 = ParticleContainer()
atoms2 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
#
atoms2.put(p4)
atoms2.put(p5)
atoms2.put(p6)
bonds1 = BondContainer()
bonds2 = BondContainer()
bonds1.put(b1)
bonds1.put(b2)
bonds2.put(b3)
bonds2.put(b4)
angles1 = AngleContainer()
angles2 = AngleContainer()
angles1.put(a1)
angles2.put(a2)
polymer1 = StructureContainer(atoms1, bonds1, angles1)
polymer2 = StructureContainer(atoms2, bonds2, angles2)
del p1, p2, p3, p4, p5, p6, b1, b2, b3, b4, a1, a2
del atoms1, atoms2, bonds1, bonds2, angles1, angles2
print "\n Cleaning memory for initial objects \n"
print "-------------------- Initial structures --------------------"
print "polymer1 = ", polymer1
print "polymer2 = ", polymer2
print " "
print "-------------- After adding (polymer1 += polymer2) ----------------"
polymer2 += polymer1
print "polymer2 = ", polymer2
def main():
"""
This test shows how to set up Structure container with Particle/Bond-Containers
Shows how ID changed in Structure propagate to values set in BondContainer and
and an AngleContainer for its held particle ID values
Illustrates how a substructure method could return subgroup
"""
print "************************************************************************************"
print " This test shows how to set up Structure container with Particle/Bond-Containers \n"
print " Shows how ID changed in Structure propagate to values set in BondContainer and "
print " and an AngleContainer for its held particle ID values \n"
print " Illustrates how a substructure method could return subgroup"
print "************************************************************************************ \n"
p1 = Particle([0.2, 1.3, 33.0], "Si", 2.0, 1.23)
p2 = Particle([5.0, 2.3, -22.1], "C", 1.0, 2.34)
p3 = Particle([5.0, 2.3, -20.1], "C", 1.0, 2.34)
p4 = Particle([0.0, 2.3, -20.1], "C", 1.0, 2.34)
p5 = Particle([0.2, 1.3, 33.0], "Si", 2.0, 1.23)
b1 = Bond(5, 2, 1.233, "hooke") # This setup mimics earlier state of test
b2 = Bond(2, 3, 0.500, "hooke") # Still matches with diagram
b3 = Bond(3, 4, 2.301, "hooke")
b4 = Bond(5, 3, 0.828, "hooke")
a1 = Angle(1, 2, 3, 1.111, "harmonic")
a2 = Angle(2, 3, 4, 2.222, "harmonic")
atoms1 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
atoms1.put(p4)
atoms1.put(p5)
del atoms1[1] # This is to mimic state of container for an older test
bonds = BondContainer()
bonds.put(b1)
bonds.put(b2)
bonds.put(b3)
bonds.put(b4)
angles = AngleContainer()
angles.put(a1)
angles.put(a2)
del p1, p2, p3, p4, b1, b2, b3, b4, a1, a2
polymer1 = StructureContainer(atoms1, bonds, angles)
del atoms1, bonds, angles
print "********************************************************** \n"
print polymer1
print diagramAfter
print "********************************************************** \n"
print "-------------------------------------------------------------------------------- \n"
print "********************************************************** \n"
print "Testing polymer1.getSubStructure([5,2])"
print " currently ID's are reassigned in substructure \n"
subpolymer = polymer1.getSubStructure([5, 2])
print subpolymer
print diagramAfter
print "********************************************************** \n"
print "********************************************************** \n"
print "polymer1 Struture after returning sub-structure"
print polymer1
print "********************************************************** \n"
print "-------------------------------------------------------------------------------- \n"
print "********************************************************** \n"
print "Testing polymer1.getSubStructure([2,3,4])"
print " currently ID's are reassigned in substructure \n"
subpolymer = polymer1.getSubStructure([2, 3, 4])
print subpolymer
print diagramAfter
print "********************************************************** \n"
