def update(self, frame_num):
pyglasstools.get_sysdata().update(frame_num)
self.cpphessian.setSystemData(
pyglasstools.get_sysdata().cppparticledata)
# if self.frame_num != frame_num:
self.cpphessian.destroyObjects()
self.cpphessian.assembleObjects()
self.frame_num = frame_num
def __init__(self, filename, names, solver):
#Save filename
self.filename = filename
#Next, parse the list of names based on what type of obsercables they are
self.__obs_names = names
#[s for s in names if "" in s or "eigenvalue" in s];
#Initialize a thermoproperty class
if solver is None:
if rank == 0:
print("[ERROR] User must specify solver object!")
comm.abort(1)
elif names is None:
if rank == 0:
print("[ERROR] User must specify list of observables to save!")
comm.abort(1)
elif filename is None:
if rank == 0:
print("[ERROR] User must specify a filename for the logfile!")
comm.abort(1)
self.solver = solver
#Once initialization is done, the logger adds itself to the global list of available loggers
loggers_list.append(self)
#write the initial files
#Initialize file to save:
self.file = _pyglasstools.MPILogFile(comm, self.filename)
#Then, add observables
self.global_obs = initialize_global(
self.__obs_names,
pyglasstools.get_sysdata().pysimbox.dim)
self.solver.add_observables(self.global_obs)
Dim = pyglasstools.get_sysdata().pysimbox.dim
#Create column headers
if rank == 0 and (
not os.path.exists(pyglasstools.get_sysdata().checkpointfile)
or
(os.path.exists(pyglasstools.get_sysdata().checkpointfile) and
os.path.getsize(pyglasstools.get_sysdata().checkpointfile) == 0)):
self.file.write_shared("{} ".format("Frame"))
if not (not self.__obs_names):
for name in self.__obs_names:
if "forcedipole_center" in name or "forcedipole_pi" in name or "forcedipole_pj" in name:
for i in range(Dim):
self.file.write_shared("{}_{} ".format(name, i))
else:
self.file.write_shared("{} ".format(name))
self.file.write_shared("\n")
def __init__(self, keyword, names, solver):
#Save filename
self.keyword = keyword
#Next, parse the list of names based on what type of obsercables they are
self.__obs_names = names
#Initialize a thermoproperty class
if solver is None:
if rank == 0:
print("[ERROR] User must specify solver object!")
comm.abort(1)
elif names is None:
if rank == 0:
print("[ERROR] User must specify list of observables to save!")
comm.abort(1)
self.solver = solver
#Once initialization is done, the logger adds itself to the global list of available loggers
loggers_list.append(self)
#write the initial files
#Then, add observables
self.field_obs = initialize_field(
self.__obs_names,
pyglasstools.get_sysdata().pysimbox.dim)
self.solver.add_observables(self.field_obs)
self.file = _pyglasstools.MPILogFile(comm,
"{}".format(keyword) + ".xyz")
def __init__(self):
#Initialize system data and pair potential of the system
self.manager = _pyglasstools.Manager()
self.thermocalculator = _thermo.ThermoCalculator(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential)
solvers_list.append(self)
def save(self, frame_num):
if rank == 0:
self.file.write_shared("{} ".format(frame_num))
for name in self.__obs_names:
Dim = pyglasstools.get_sysdata().pysimbox.dim
if "potentialenergy" in name:
self.global_obs['potentialenergy'].save(self.file, 0)
self.file.write_shared(" ")
if "virialstress" in name:
i = int(name[-2])
j = int(name[-1])
self.global_obs['virialstress'].save(
self.file, i + Dim * j)
self.file.write_shared(" ")
elif "kineticstress" in name:
i = int(name[-2])
j = int(name[-1])
self.global_obs['kineticstress'].save(
self.file, i + Dim * j)
self.file.write_shared(" ")
elif "borntensor" in name:
i = int(name[-4])
j = int(name[-3])
k = int(name[-2])
l = int(name[-1])
#self.global_obs['borntensor'].save(self.file,i+Dim*(j+Dim*(k+Dim*l)))
self.global_obs['borntensor'].save(
self.file, l + Dim * (k + Dim * (j + Dim * i)))
self.file.write_shared(" ")
self.file.write_shared("\n")
def save(self, frame_num):
if self.solver.pyhessian.check_diagonals():
if rank == 0:
self.file.write_shared("{:d} \n".format(
len(pyglasstools.get_sysdata().traj[frame_num].particles.
position)))
self.file.write_shared("#Frame {:d} \n".format(frame_num))
comm.barrier()
self.save_perrank(frame_num)
def __init__(self, cgfunc, dx):
self.cgfunc = cgfunc
self.manager = _pyglasstools.Manager()
self.coordmode = "cartesian"
#Maybe move it to C++ side . . . .
globalsize = 0
if rank == 0:
nmax = int(pyglasstools.get_sysdata().pysimbox.boxsize[0] / dx)
points = np.linspace(
-pyglasstools.get_sysdata().pysimbox.boxsize[0] / 2.0,
+pyglasstools.get_sysdata().pysimbox.boxsize[0] / 2.0, nmax)
gridpoints = []
for i in range(len(points)):
for j in range(len(points)):
gridpoints.append(
np.asarray([points[i], points[j], 0],
dtype=np.float64))
globalsize = len(gridpoints)
self.gridpoints = np.array_split(
np.asarray(gridpoints, dtype=np.float64), size)
del points, nmax
else:
self.gridpoints = np.array_split([np.zeros(size)], size)
#Scatter and reshape
self.gridpoints = comm.scatter_v(self.gridpoints, 0)
self.gridpoints = np.reshape(self.gridpoints,
(len(self.gridpoints), 3))
#Broadcast the true size
self.gridsize = comm.bcast(globalsize, 0)
self.calculator = _irvingkirkwood.IrvingKirkwood(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential, cgfunc._getCGFunc(),
comm)
solvers_list.append(self)
def save_perrank(self, frame_num):
Dim = pyglasstools.get_sysdata().pysimbox.dim
ave, res = divmod(
len(pyglasstools.get_sysdata().traj[frame_num].particles.position),
size)
counts = [ave + 1 if p < res else ave for p in range(size)]
# determine the starting and ending indices of each sub-task
starts = [sum(counts[:p]) for p in range(size)]
ends = [sum(counts[:p + 1]) for p in range(size)]
# converts data into a list of arrays
#Do scatter for each held eigenvectors
for name in self.__obs_names:
if "eigenvector" in name:
self.field_obs[name].scatterVector(starts[rank], counts[rank])
for i in range(starts[rank], ends[rank]):
outline = "{} ".format(1)
outline += "{} ".format(
pyglasstools.get_sysdata().traj[frame_num].particles.position[
i, 0])
outline += "{} ".format(
pyglasstools.get_sysdata().traj[frame_num].particles.position[
i, 1])
if Dim == 3:
outline += "{} ".format(pyglasstools.get_sysdata(
).traj[frame_num].particles.position[i, 2])
for name in self.__obs_names:
flattenindex = 0
if "forcedipole" in name:
outline += self.field_obs["forcedipole"].gettostring(i)
if "eigenvector" in name:
outline += self.field_obs[name].gettostring(i -
starts[rank])
outline += "\n"
self.file.write_shared(outline)
def get_vectorfield(self, name, frame_num):
vector = []
ave, res = divmod(
len(pyglasstools.get_sysdata().traj[frame_num].particles.position),
size)
counts = [ave + 1 if p < res else ave for p in range(size)]
starts = sum(counts[:rank])
ends = sum(counts[:rank + 1])
for i in range(starts, ends):
vector.append(
np.reshape(self.field_obs[name].getVectorValue(i), (3, )))
#Next, we gather all of these vectors
newvector = comm.all_gather_v(vector)
vector = [item for sublist in newvector for item in sublist]
#vector = np.reshape(newvector,(len(pyglasstools.get_sysdata().traj[frame_num].particles.position),3));
del newvector
return vector #Reshape
def save_perrank_polar(self, frame_num):
Dim = pyglasstools.get_sysdata().pysimbox.dim
for index, gridpos in enumerate(self.solver.gridpoints):
outline = "{} ".format(1)
outline += "{} ".format(int(self.solver.gridid[index]))
outline += "{} ".format(self.solver.globalr[index])
outline += "{} ".format(self.solver.globaltheta[index])
for name in self.__obs_names:
flattenindex = 0
if "stress" in name:
i = int(name[-2])
j = int(name[-1])
flattenindex = i + Dim * j
outline += self.field_obs[name[:-3]].gettostring(
i + Dim * j, index)
outline += "\n"
self.file.write_shared(outline)
def save(self, frame_num):
if rank == 0 and self.solver.pyhessian.check_diagonals():
self.file.write_shared("{} ".format(frame_num))
for name in self.__obs_names:
Dim = pyglasstools.get_sysdata().pysimbox.dim
if "forcedipole" in name:
for i in range(Dim):
self.global_obs[name].save(self.file, i)
self.file.write_shared(" ")
if "eigenvalue" in name or "nconv" in name or "eigenrelerr" in name:
self.global_obs[name].save(self.file)
if "nonaffinetensor" in name:
i = int(name[-4])
j = int(name[-3])
k = int(name[-2])
l = int(name[-1])
self.global_obs['nonaffinetensor'].save(
self.file, l + Dim * (k + Dim * (j + Dim * i)))
self.file.write_shared(" ")
self.file.write_shared("\n")
def __init__(self, package):
#Initialize system data and pair potential of the system
self.package = package
self.cppmanager = _elasticity.PETScManager()
dimensions = pyglasstools.get_sysdata().pysimbox.dim
if (package == "petsc"):
if dimensions == 2:
self.cpphessian = _elasticity.PETScHessian2D(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential,
self.cppmanager, comm)
else:
self.cpphessian = _elasticity.PETScHessian3D(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential,
self.cppmanager, comm)
elif (package == "slepc"):
if dimensions == 2:
self.cpphessian = _elasticity.SLEPcHessian2D(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential,
self.cppmanager, comm)
else:
self.cpphessian = _elasticity.SLEPcHessian3D(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential,
self.cppmanager, comm)
elif (package == "spectra"):
if dimensions == 2:
self.cpphessian = _elasticity.SpectraHessian2D(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential,
self.cppmanager, comm)
else:
self.cpphessian = _elasticity.SpectraHessian3D(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential,
self.cppmanager, comm)
self.frame_num = pyglasstools.get_sysdata().frame_num
def update(self, frame_num):
pyglasstools.update_sysdata(frame_num)
self.calculator.setSystemData(
pyglasstools.get_sysdata().cppparticledata)
def __init__(self,
cgfunc,
center=np.array([0, 0, 0]),
spacingtype="normal",
rmax=10,
rmin=0,
dr=0.1,
dlnr=0.05):
self.cgfunc = cgfunc
self.manager = _pyglasstools.Manager()
self.coordmode = "polar"
#TO DO: Move all of this hassle to C++ side . . . .
globalsize = 0
self.center = center
if rank == 0:
gridpoints = []
if spacingtype == "normal":
r = np.linspace(0, rmax, int(rmax / dr))[1:]
elif spacingtype == "log":
r = np.exp(
np.linspace(np.log(rmin), np.log(rmax),
int((np.log(rmax) - np.log(rmin)) / dlnr)))
gridid = [] #id based on radius
globalr = []
globaltheta = []
gridpoints = []
#Append the origin
gridid.append(0)
globalr.append(0)
globaltheta.append(0)
gridpoints.append(self.center)
for i in range(len(r)):
dtheta = dr / r[i]
theta = np.linspace(0, 2 * np.pi, int(2 * np.pi / dtheta))
x = r[i] * np.cos(theta)
y = r[i] * np.sin(theta)
for j in range(len(theta)):
gridid.append(i + 1)
globalr.append(r[i])
globaltheta.append(theta[j])
gridpoints.append(
np.asarray([x[j], y[j], 0], dtype=np.float64) +
self.center)
globalsize = len(gridpoints)
#print(np.shape(gridpoints),np.shape(center))
self.gridid = np.array_split(np.asarray(gridid, dtype=np.float64),
size)
self.globalr = np.array_split(
np.asarray(globalr, dtype=np.float64), size)
self.globaltheta = np.array_split(
np.asarray(globaltheta, dtype=np.float64), size)
self.gridpoints = np.array_split(
np.asarray(gridpoints, dtype=np.float64), size)
del r, theta, dtheta, x, y, gridpoints, gridid, globalr, globaltheta
else:
self.gridid = np.array_split(np.zeros(size), size)
self.globalr = np.array_split(np.zeros(size), size)
self.globaltheta = np.array_split(np.zeros(size), size)
self.gridpoints = np.array_split([np.zeros(size)], size)
#Scatter and reshape
self.gridid = comm.scatter_v(self.gridid, 0)
self.gridid = np.reshape(self.gridid, (len(self.gridid), ))
#Scatter and reshape
self.globalr = comm.scatter_v(self.globalr, 0)
self.globalr = np.reshape(self.globalr, (len(self.globalr), ))
#Scatter and reshape
self.globaltheta = comm.scatter_v(self.globaltheta, 0)
self.globaltheta = np.reshape(self.globaltheta,
(len(self.globaltheta), ))
#Scatter and reshape
self.gridpoints = comm.scatter_v(self.gridpoints, 0)
self.gridpoints = np.reshape(self.gridpoints,
(len(self.gridpoints), 3))
#Broadcast the true size
self.gridsize = comm.bcast(globalsize, 0)
#del globalsize
self.calculator = _irvingkirkwood.IrvingKirkwood(
pyglasstools.get_sysdata().cppparticledata,
pyglasstools.get_potential().cpppairpotential, cgfunc._getCGFunc(),
comm)
solvers_list.append(self)