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database.py
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database.py
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import numpy as np
import h5py
from utils import rotation_matrix,rotate_tensor2
class AxiBasicDB:
def __init__(self) -> None:
pass
def read_basic(self,ncfile:str) -> None:
"""
ncfile : str
input netcdf file
"""
# load library
from scipy.spatial import KDTree
fio:h5py.File = h5py.File(ncfile,"r")
self.nspec = len(fio['Mesh/elements'])
self.nctrl = len(fio['Mesh/control_points'])
self.ngll = len(fio['Mesh/npol'])
# read attributes
self.dtsamp = fio.attrs['strain dump sampling rate in sec'][0]
self.shift = fio.attrs['source shift factor in sec'][0]
self.nt = len(fio['snapshots'])
self.nglob = len(fio['gllpoints_all'])
self.t0 = fio.attrs['dump_t0']
# read source parameters
self.evdp = fio.attrs['source depth in km'][0] * 1.
evcola = fio.attrs['Source colatitude'][0]
evlo = fio.attrs['Source longitude'][0]
self.evla:float = 90 - np.rad2deg(evcola)
self.evlo:float = np.rad2deg(evlo)
self.mag = fio.attrs['scalar source magnitude'][0] * 1.
# rotation matrix
self.rot_mat = rotation_matrix(evcola,evlo)
# read mesh
self.mesh_s = fio['Mesh/mesh_S'][:]
self.mesh_z = fio['Mesh/mesh_Z'][:]
# create kdtree
md_pts = np.zeros((self.nspec,2))
md_pts[:,0] = fio['Mesh/mp_mesh_S'][:]
md_pts[:,1] = fio['Mesh/mp_mesh_Z'][:]
self.kdtree = KDTree(data=md_pts)
# elemtype
self.eltype = fio['Mesh/eltype'][:]
self.axis = fio['Mesh/axis'][:]
# skeleton
self.skelid = fio['Mesh/fem_mesh'][:]
# connectivity[
self.ibool = fio['Mesh/sem_mesh'][:]
# other useful arrays
self.G0 = fio['Mesh/G0'][:]
self.G1 = fio['Mesh/G1'][:].T
self.G2 = fio['Mesh/G2'][:].T
self.G1T = np.require(self.G1.T,requirements=['F_CONTIGUOUS'])
self.G2T = np.require(self.G2.T,requirements=['F_CONTIGUOUS'])
self.gll = fio['Mesh/gll'][:]
self.glj = fio['Mesh/glj'][:]
# elastic moduli
self.mu = fio['Mesh/mesh_mu'][:]
self.lamda = fio['Mesh/mesh_lambda'][:]
# close file
fio.close()
# data file dict
self.iodict = {}
def __copy__(self):
"""
shallow copy of necessary basic variables
"""
db = AxiBasicDB()
# shallow copy of necessary variables
db.nspec = self.nspec
db.nctrl = self.nctrl
db.ngll = self.ngll
# attributes
db.dtsamp = self.dtsamp
db.shift = self.shift
db.nt = self.nt
db.nglob = self.nglob
db.t0 = self.t0
# source parameters
db.evdp = self.evdp
db.evla = self.evla
db.evlo = self.evlo
db.mag = self.mag
# rotation matrix
db.rot_mat = self.rot_mat * 1.
# read mesh
db.mesh_s = self.mesh_s
db.mesh_z = self.mesh_z
# create kdtree
db.kdtree = self.kdtree
# elemtype
db.eltype = self.eltype
db.axis = self.axis
# skeleton
db.skelid = self.skelid
# connectivity[
db.ibool = self.ibool
# deep copy useful arrays
db.G0 = self.G0.copy()
db.G1 = self.G1.copy()
db.G2 = self.G2.copy()
db.G1T = self.G1T.copy()
db.G2T = self.G2T.copy()
db.gll = self.gll.copy()
db.glj = self.glj.copy()
# elastic moduli
db.mu = self.mu
db.lamda = self.lamda
# data file dict
db.iodict = {}
return db
def set_iodata(self,ncfile_dir:str):
"""
set absolute path to top simulation dir
Example:
set_iodata('/path/to/axisem/solver/simudir')
)
"""
import os
for stype in ['MZZ',"MXX_P_MYY","MXZ_MYZ","MXY_MXX_M_MYY","PZ","PX","PY"]:
dirname = ncfile_dir + '/' + stype
if os.path.exists(dirname):
self.iodict[stype] = h5py.File(dirname + '/Data/axisem_fields.h5',"r")
# check if iodit is empty
if len(self.iodict) == 0 :
print(f"no data has been accessed, please check {ncfile_dir}!")
def copy(self):
return self.__copy__()
def close(self):
for _,val in self.iodict.items():
val.close()
self.iodict = {}
def set_source(self,evla:float,evlo:float):
"""
update source info in the database
evla: float
latitude of station, in deg
evlo: float
longitude of station, in deg
"""
self.evla = evla
self.evlo = evlo
self.rot_mat = rotation_matrix(np.pi/2-np.deg2rad(evla),np.deg2rad(evlo))
pass
def read_cmt(self,cmtfile:str):
from utils import read_cmtsolution
mzz,mxx,myy,mxz,myz,mxy = read_cmtsolution(cmtfile)
mzz,mxx,myy,mxz,myz,mxy = map(lambda x: x / self.mag,[mzz,mxx,myy,mxz,myz,mxy])
return mzz,mxx,myy,mxz,myz,mxy
def _locate_elem(self,s,z):
from sem_funcs import inside_element
id_elem = None
# get nearest 10 points
points = self.kdtree.query([s,z],k=10)[1]
for tol in [1e-3, 1e-2, 5e-2, 8e-2]:
for idx in points:
skel = np.zeros((self.nctrl,2))
ctrl_id = self.skelid[idx,:]
eltype = self.eltype[idx]
for i in range(self.nctrl):
skel[i,0] = self.mesh_s[ctrl_id[i]]
skel[i,1] = self.mesh_z[ctrl_id[i]]
isin,xi,eta = inside_element(s,z,skel,eltype,tolerance=tol)
if isin:
id_elem = idx
break;
if id_elem is not None:
break
return id_elem,xi,eta
def _get_displ(self,elemid,xi,eta,stype):
"""
Get displacement for one station
stel: float
elevation, in m
theta: float
epicenter distance, in rad
ncfile: str
ncfile which the displ is stored in
Returns:
us,up,uz: np.ndarray
s,p,z components
"""
from sem_funcs import lagrange_interpol_2D_td
nt = self.nt
# allocate space
us = np.zeros((nt)); up = us * 0; uz = us * 1.
# dataset info
fio:h5py.File = self.iodict[stype]
ngll = fio['disp_s'].shape[1]
utemp = np.zeros((3,ngll,ngll,nt),dtype=float)
# read dataset
utemp[0,...] = fio['disp_s'][elemid,...]
utemp[2,...] = fio['disp_z'][elemid,...]
if 'disp_p' in fio.keys():
utemp[1,...] = fio['disp_p'][elemid,...]
utemp = np.transpose(utemp,(3,2,1,0))
sgll = self.gll
zgll = self.gll
flag = self.axis[elemid] == 1
if flag:
sgll = self.glj
us = lagrange_interpol_2D_td(sgll,zgll,utemp[:,:,:,0],xi,eta)
up = lagrange_interpol_2D_td(sgll,zgll,utemp[:,:,:,1],xi,eta)
uz = lagrange_interpol_2D_td(sgll,zgll,utemp[:,:,:,2],xi,eta)
return us,up,uz
def _get_excitation_type(self,stype:str) -> str :
if stype in ['MZZ',"PZ",'MXX_P_MYY']:
return 'monopole'
elif stype in ['MXZ_MYZ',"PX","PY"]:
return 'dipole'
else:
return 'quadpole'
def _get_strain(self,elemid:int,xi:float,eta:float,stype:str):
"""
get strain field at a given point, for a given source type
Parameters:
===================================================
elemid: current
xi/eta: local coordinates
stype: source type
Returns:
====================================================
strain : np.ndarray
shape(6,nt), ess,epp,ezz,epz,esz,esp
"""
from sem_funcs import lagrange_interpol_2D_td,strain_td
nt = self.nt
fio:h5py.File = self.iodict[stype]
ngll = fio['disp_s'].shape[1]
# allocate space
eps = np.zeros((6,nt))
# cache element
utemp = np.zeros((3,ngll,ngll,nt),dtype=float)
# dataset
# read dataset
utemp[0,...] = fio['disp_s'][elemid,...]
utemp[2,...] = fio['disp_z'][elemid,...]
if 'disp_p' in fio.keys():
utemp[1,...] = fio['disp_p'][elemid,...]
utemp = np.transpose(utemp,(3,2,1,0))
# gll/glj array
sgll = self.gll
zgll = self.gll
is_axi = self.axis[elemid] == 1
if is_axi:
sgll = self.glj
# control points
skel = np.zeros((self.nctrl,2))
ctrl_id = self.skelid[elemid,:]
eltype = self.eltype[elemid]
skel[:,0] = self.mesh_s[ctrl_id]
skel[:,1] = self.mesh_z[ctrl_id]
if is_axi:
G = self.G2
GT = self.G1T
else:
G = self.G2
GT = self.G2T
# compute strain shape(nt,npol+1,npol+1,6)
etype = self._get_excitation_type(stype)
strain = strain_td(utemp,G,GT,sgll,zgll,ngll-1,nt,
skel,eltype,is_axi,etype)
# interpolate
# es shape(6,nt)
for j in range(6):
eps[j,:] = lagrange_interpol_2D_td(sgll,zgll,strain[:,:,:,j],xi,eta)
return eps
def _get_stress(self,elemid,xi,eta,stype):
"""
get stress field for a given point from file
Returns:
stress : np.ndarray
shape(6,nt), ess,epp,ezz,epz,esz,esp
"""
from sem_funcs import lagrange_interpol_2D_td,strain_td
nt = self.nt
fio:h5py.File = self.iodict[stype]
ngll = fio['disp_s'].shape[1]
# cache element
utemp = np.zeros((3,ngll,ngll,nt),dtype=float)
# dataset
utemp[0,...] = fio['disp_s'][elemid,...]
utemp[2,...] = fio['disp_z'][elemid,...]
if 'disp_p' in fio.keys():
utemp[1,...] = fio['disp_p'][elemid,...]
utemp = np.transpose(utemp,(3,2,1,0))
# alloc arrays for mu and lambda
xmu = np.zeros((ngll,ngll),dtype=float)
xlam = np.zeros((ngll,ngll),dtype=float)
xmu[:,:] = self.mu[elemid,:,:]
xlam[:,:] = self.lamda[elemid,:,:]
xmu = np.transpose(xmu)
xlam = np.transpose(xlam)
# gll/glj array
sgll = self.gll
zgll = self.gll
is_axi = self.axis[elemid] == 1
if is_axi:
sgll = self.glj
# control points
skel = np.zeros((self.nctrl,2))
ctrl_id = self.skelid[elemid,:]
eltype = self.eltype[elemid]
skel[:,0] = self.mesh_s[ctrl_id]
skel[:,1] = self.mesh_z[ctrl_id]
if self.axis[elemid]:
G = self.G2
GT = self.G1T
else:
G = self.G2
GT = self.G2T
# compute strain shape(nt,npol+1,npol+1,6)
etype = self._get_excitation_type(stype)
strain = strain_td(utemp,G,GT,sgll,zgll,ngll-1,self.nt,
skel,eltype,self.axis[elemid]==1,etype)
# compute stress
stress = strain * 0.
stress[...,0] = (xlam + 2 * xmu) * strain[...,0] + xlam * (strain[...,1] + strain[...,2])
stress[...,1] = (xlam + 2 * xmu) * strain[...,1] + xlam * (strain[...,0] + strain[...,2])
stress[...,2] = (xlam + 2 * xmu) * strain[...,2] + xlam * (strain[...,0] + strain[...,1])
stress[...,3] = 2. * xmu * strain[...,3]
stress[...,4] = 2. * xmu * strain[...,4]
stress[...,5] = 2. * xmu * strain[...,5]
# interpolate
# es shape(6,nt)
sigma = np.zeros((6,nt))
for j in range(6):
sigma[j,:] = lagrange_interpol_2D_td(sgll,zgll,stress[:,:,:,j],xi,eta)
return sigma
def compute_tp_recv(self,stla,stlo):
"""
compute theta and phi for source centered coordinates
stla: float
latitude of station, in deg
stlo: float
longitude of station, in deg
"""
x = np.cos(stla * np.pi/180) * np.cos(stlo * np.pi/180)
y = np.cos(stla * np.pi/180) * np.sin(stlo * np.pi/180)
z = np.sin(stla * np.pi/ 180)
# rotate xyz to source centered system
x1,y1,z1 = np.dot(self.rot_mat.T,np.array([x,y,z]))
# to phi and theta
r = np.sqrt(x1**2 + y1**2 + z1**2)
x1 /=r; y1 /= r; z1 /= r
#r = np.sqrt(x1**2 + y1**2)
theta = np.arccos(z1/r)
phi = np.arctan2(y1,x1)
# if phi < 0:
# phi = np.pi - phi
return theta,phi
def compute_local(self,theta,stel):
"""
compute local coordinates in axisem system
theta float
epicenter distance, in rad
stel: float
elevation of the station, in m
"""
# locate point
r = 6371000 + stel
sr = r * np.sin(theta)
zr = r * np.cos(theta)
return sr,zr
def syn_seismo(self,stla,stlo,stel,comp:str='enz',cmtfile=None,forcevec=None):
"""
comp: Specify the orientation of the synthetic seismograms as a list
one of [enz,xyz,spz]
"""
# check components
comp = comp.lower()
assert(comp in ['enz','xyz','spz'])
# read source type
assert((cmtfile is not None) or (forcevec is not None))
mzz,mxx,myy,mxz,myz,mxy = [0. for i in range(6)]
fx,fy,fz = [0.,0.,0.]
srctypes = []
if cmtfile is not None:
mzz,mxx,myy,mxz,myz,mxy = self.read_cmt(cmtfile)
srctypes = ['MZZ',"MXX_P_MYY","MXZ_MYZ","MXY_MXX_M_MYY"]
else:
fx,fy,fz = forcevec
srctypes = ["PZ","PX","PY"]
# alloc space for seismograms
nt = self.nt
us = np.zeros((nt))
uz = us.copy(); up = us.copy()
# compute rotated station phi,theta
theta,phi = self.compute_tp_recv(stla,stlo)
sr,zr = self.compute_local(theta,stel)
# locate element
elemid,xi,eta = self._locate_elem(sr,zr)
# loop every source type
for stype in srctypes:
#print("synthetic seismograms for ... %s" %(stype))
# get basic waveform
us1,up1,uz1 = self._get_displ(elemid,xi,eta,stype)
# parameters
a = 0.; b = 0.
if stype == 'MZZ': # mono
a = mzz
b = 0.
elif stype == "PZ":
a = fz
b = 0.
elif stype == 'MXX_P_MYY': # mono
a = mxx + myy
b = 0
# interpolate
cosphi = np.cos(phi); sinphi = np.sin(phi)
cos2phi = np.cos(2 * phi); sin2phi = np.sin(2 * phi)
if stype == 'MXZ_MYZ':
a = mxz * cosphi + myz * sinphi
b = myz * cosphi - mxz * sinphi
elif stype == "MXY_MXX_M_MYY":
a = (mxx - myy) * cos2phi + 2 * mxy * sin2phi
b = -(mxx - myy) * sin2phi + 2 * mxy * cos2phi
elif stype == 'PX' or stype == "PY":
a = fx * cosphi + fy * sinphi
b = -fx * sinphi + fy * cosphi
# normalize
us1[:] *= a; up1[:] *= b; uz1[:] *= a
# add contribution from each term
us += us1
up += up1
uz += uz1
# rotate to specified coordinates
u1 = uz * 0.; u2 = up * 0.; u3 = up * 0.
# rotation matrix to enz
R1 = np.eye(3) # rotate from (s,phi,z) to (xs,ys,z)
R1[0,:2] = [np.cos(phi),-np.sin(phi)]
R1[1,:2] = [np.sin(phi),np.cos(phi)]
Rr = rotation_matrix(np.deg2rad(90-stla),np.deg2rad(stlo))
if comp == 'enz':
Rr = Rr.T @ self.rot_mat @ R1
elif comp == 'spz':
Rr = np.eye(3)
else:
Rr = self.rot_mat @ R1
u1 = Rr[0,0] * us + Rr[0,1] * up + Rr[0,2] * uz
u2 = Rr[1,0] * us + Rr[1,1] * up + Rr[1,2] * uz
u3 = Rr[2,0] * us + Rr[2,1] * up + Rr[2,2] * uz
if comp == 'enz':
u1 = -u1
temp = u1.copy()
u1 = u2.copy()
u2 = temp.copy()
return u1,u2,u3
def syn_strain(self,stla,stlo,stel,cmtfile=None,forcevec=None):
# read source type
assert((cmtfile is not None) or (forcevec is not None))
mzz,mxx,myy,mxz,myz,mxy = [0. for i in range(6)]
fx,fy,fz = [0.,0.,0.]
srctypes = []
if cmtfile is not None:
mzz,mxx,myy,mxz,myz,mxy = self.read_cmt(cmtfile)
srctypes = ['MZZ',"MXX_P_MYY","MXZ_MYZ","MXY_MXX_M_MYY"]
else:
fx,fy,fz = forcevec
srctypes = ["PZ","PX_PY"]
# alloc space for seismograms
nt = self.nt
eps = np.zeros((6,nt))
# compute rotated station phi,theta
theta,phi = self.compute_tp_recv(stla,stlo)
sr,zr = self.compute_local(theta,stel)
# locate element
elemid,xi,eta = self._locate_elem(sr,zr)
# loop every source type
for stype in srctypes:
#print("synthetic strain tensor for ... %s" %(stype))
# get basic waveform
eps0 = self._get_strain(elemid,xi,eta,stype)
# parameters
a = 0.; b = 0.
if stype == 'MZZ': # mono
a = mzz
b = 0.
elif stype == "PZ":
a = fz
b = 0.
elif stype == 'MXX_P_MYY': # mono
a = mxx + myy
b = 0
# interpolate
cosphi = np.cos(phi); sinphi = np.sin(phi)
cos2phi = np.cos(2 * phi); sin2phi = np.sin(2 * phi)
if stype == 'MXZ_MYZ':
a = mxz * cosphi + myz * sinphi
b = myz * cosphi - mxz * sinphi
elif stype == "MXY_MXX_M_MYY":
a = (mxx - myy) * cos2phi + 2 * mxy * sin2phi
b = -(mxx - myy) * sin2phi + 2 * mxy * cos2phi
elif stype == "PX_PY":
a = fx * cosphi + fy * sinphi
b = -fx * sinphi + fy * cosphi
# normalize
# eps: ss pp zz pz sz sp
eps0[0:3,:] *= a; eps0[4,:] *= a
eps0[3,:] *= b; eps0[5:,:] *= b
# add contribution from each term
eps += eps0
# rotate to xyz
R1 = np.eye(3) # rotate from (s,phi,z) to (xs,ys,z)
R1[0,:2] = [np.cos(phi),-np.sin(phi)]
R1[1,:2] = [np.sin(phi),np.cos(phi)]
R = self.rot_mat @ R1
eps_xyz = rotate_tensor2(eps,R)
return eps_xyz
def syn_stress(self,stla,stlo,stel,cmtfile=None,forcevec=None):
# read source type
assert((cmtfile is not None) or (forcevec is not None))
mzz,mxx,myy,mxz,myz,mxy = [0. for i in range(6)]
fx,fy,fz = [0.,0.,0.]
srctypes = []
if cmtfile is not None:
mzz,mxx,myy,mxz,myz,mxy = self.read_cmt(cmtfile)
srctypes = ['MZZ',"MXX_P_MYY","MXZ_MYZ","MXY_MXX_M_MYY"]
else:
fx,fy,fz = forcevec
srctypes = ["PZ","PX_PY"]
# alloc space for seismograms
nt = self.nt
sigma = np.zeros((6,nt))
# compute rotated station phi,theta
theta,phi = self.compute_tp_recv(stla,stlo)
sr,zr = self.compute_local(theta,stel)
# locate element
elemid,xi,eta = self._locate_elem(sr,zr)
# loop every source type
for stype in srctypes:
#print("synthetic strain tensor for ... %s" %(stype))
# get basic waveform
eps0 = self._get_stress(elemid,xi,eta,stype)
# parameters
a = 0.; b = 0.
if stype == 'MZZ': # mono
a = mzz
b = 0.
elif stype == "PZ":
a = fz
b = 0.
elif stype == 'MXX_P_MYY': # mono
a = mxx + myy
b = 0
# interpolate
cosphi = np.cos(phi); sinphi = np.sin(phi)
cos2phi = np.cos(2 * phi); sin2phi = np.sin(2 * phi)
if stype == 'MXZ_MYZ':
a = mxz * cosphi + myz * sinphi
b = myz * cosphi - mxz * sinphi
elif stype == "MXY_MXX_M_MYY":
a = (mxx - myy) * cos2phi + 2 * mxy * sin2phi
b = -(mxx - myy) * sin2phi + 2 * mxy * cos2phi
elif stype == "PX_PY":
a = fx * cosphi + fy * sinphi
b = -fx * sinphi + fy * cosphi
# normalize
eps0[0:3,:] *= a; eps0[4,:] *= a
eps0[3,:] *= b; eps0[5:,:] *= b
# add contribution from each term
sigma += eps0
# rotate to xyz
R1 = np.eye(3) # rotate from (s,phi,z) to (xs,ys,z)
R1[0,:2] = [np.cos(phi),-np.sin(phi)]
R1[1,:2] = [np.sin(phi),np.cos(phi)]
R = self.rot_mat @ R1
sigma_xyz = rotate_tensor2(sigma,R)
return sigma_xyz