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Copy pathread_stride_utils.py
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700 lines (545 loc) · 22.8 KB
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import numpy as np
import os
import sys
import subprocess
from gfile_helpers import write_gfile
import time
def percent_err(x,y):
return 100*np.abs(x-y)/(np.abs(x) + np.abs(y) + np.finfo(np.float32).eps)
def flatten(x):
"""Flattens a nested list or tuple
Args:
x (list or tuple): nested list or tuple of lists or tuples to flatten
Returns:
x (list): flattened input
"""
if isinstance(x, list) or isinstance(x, tuple):
return [a for i in x for a in flatten(i)]
else:
return [x]
def str2complex(s):
"""parses strings of the form (re,im) into complex numbers"""
re = float(s[1:-1].split(',')[0])
im = float(s[1:-1].split(',')[1])
return complex(re,im)
def str2complex2(s):
"""parses strings of the form re +i*im into complex numbers"""
for i, char in enumerate(s):
if char == 'i' or char == 'j':
idx = i
sign = s[idx-1]
real = float(s[:idx-1])
imag = float(s[idx+2:]) * (1 if sign == '+' else -1)
return complex(real,imag)
def parse_raw_output(raw_output, return_timing=True, return_interval_details=True):
"""reads terminal output of original code, to get locations of singularities and other related quantities"""
if isinstance(raw_output,list):
f = flatten(raw_output)
else:
f = raw_output.split('\n')
psio = float([foo.split()[-1] for foo in f if 'psio = ' in foo][0])
mpsi = int([foo.split()[-1] for foo in f if 'mpsi = ' in foo][0])
mtheta = int([foo.split()[-1] for foo in f if 'mtheta = ' in foo][0])
mdata = [foo for foo in f if "mband" in foo][0].split()
mlow = int([mdata[i+2] for i in range(len(mdata)-2) if 'mlow' in mdata[i]][0][:-1])
mhigh = int([mdata[i+2] for i in range(len(mdata)-2) if 'mhigh' in mdata[i]][0][:-1])
nn = int([mdata[i+2] for i in range(len(mdata)-2) if 'nn' in mdata[i]][0][:-1])
singid = []
singpsi = []
singm = []
if return_interval_details:
raw_interval_details = [foo for foo in f if foo.startswith('Interval')]
interval_details = {'interval': np.array([int(foo.split()[1]) for foo in raw_interval_details]),
'nsteps': np.array([int(foo.split()[3]) for foo in raw_interval_details]),
'nfevals': np.array([int(foo.split()[5]) for foo in raw_interval_details]),
'startpsi': np.array([float(foo.split()[7]) for foo in raw_interval_details]),
'endpsi': np.array([float(foo.split()[9]) for foo in raw_interval_details]),
'interval_time': np.array([float(foo.split()[11]) for foo in raw_interval_details]),
}
interval_details['flops'] = 38/3*interval_details['nfevals'] + 4
else:
interval_details = None
if return_timing:
times = {'equil': float([foo for foo in f if '*** equil-input time=' in foo][0].split()[-1]),
'locstab': float([foo for foo in f if '*** locstab time=' in foo][0].split()[-1]),
'sing': float([foo for foo in f if '*** sing time=' in foo][0].split()[-1]),
'fourfit': float([foo for foo in f if '*** fourfit-tot time=' in foo][0].split()[-1]),
'threadalloc': float([foo for foo in f if '*** thread-alloc time=' in foo][0].split()[-1]),
'integration': float([foo for foo in f if '*** ode-parallel-integration time=' in foo][0].split()[-1]),
'propagation': float([foo for foo in f if '*** ode-propagateLR time=' in foo][0].split()[-1]),
'wpmodes': float([foo for foo in f if '*** calc-modes-for-wp time=' in foo][0].split()[-1]),
'wpcalc': float([foo for foo in f if '*** wp-calc time=' in foo][0].split()[-1]),
'free': float([foo for foo in f if '*** free-run time=' in foo][0].split()[-1]),
'parallel': float([foo for foo in f if '*** tot-parallel time=' in foo][0].split()[-1]),
'total': float([foo for foo in f if '*** complete-run time=' in foo][0].split()[-1]),
}
else:
times = None
for i, line in enumerate(f):
if 'Sing# = ' in line:
singid.append(int(f[i].split()[-1]))
singpsi.append(float(f[i+3].split()[-1]))
singm.append(int(f[i+2].split()[-1]))
singinterval = [line for line in f if ' sing # ' in line]
singstarts = [float(foo.split()[-2]) for foo in singinterval]
singends = [float(foo.split()[-1]) for foo in singinterval]
m_grid = np.arange(mlow,mhigh+1)
sing = np.array([singstarts,singends,singm]).T
sing_loc = np.array([0,*singpsi,1])
return sing, sing_loc, m_grid, mpsi, mtheta, nn, psio, times, interval_details
def readWmat(filename,M):
"""Reads results of original code"""
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
temp = np.array([str2complex(elem) for elem in f])
W_dcon = temp.reshape((M,M),order='f')
return W_dcon
def readLmat(filename):
"""Reads values of psi and ODE RHS matrix L(psi) from text file generated by original code"""
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_idx = []
for i, line in enumerate(f):
if '(' not in line:
psi_idx.append(i)
psi_idx = np.array(psi_idx)
nsteps = len(psi_idx)
np.testing.assert_almost_equal(np.std(np.diff(psi_idx)),0,err_msg='Unequal matrix sizes at different psi locations!')
N = np.sqrt(np.diff(psi_idx)[0]-1)
np.testing.assert_almost_equal(N,int(N),err_msg='Non square matrices!')
N = int(N)
M = int(N/2)
psi = np.full((nsteps,),np.nan,dtype=np.float64)
Ldata = np.full((nsteps,N,N),np.nan,dtype=np.complex128)
for i, idx in enumerate(psi_idx):
psi[i] = float(f[idx])
temp = f[idx+1:idx+N**2+1]
temp = np.array([str2complex(elem) for elem in temp])
Ldata[i] = temp.reshape((N,N),order='f')
assert not np.any(np.isnan(psi))
assert not np.any(np.isnan(Ldata))
idx = np.argsort(psi)
psi = psi[idx]
Ldata = Ldata[idx]
L = {'psi_grid':psi,
'L':Ldata}
return L
def read_primitive_matrices(directory,M):
matrices = {}
filenames = [foo + 'mat.out' for foo in 'abcdeh']
for filename in filenames:
with open(directory + '/' + filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_idx = []
for i, line in enumerate(f):
if '(' not in line:
psi_idx.append(i)
psi_idx = np.array(psi_idx)
nsteps = len(psi_idx)
np.testing.assert_almost_equal(np.std(np.diff(psi_idx)),0,err_msg='Unequal matrix sizes at different psi locations!')
mat_id = filename[0].upper()
matrices[mat_id] = np.full((nsteps,M,M),np.nan,dtype=np.complex128)
matrices['psi_' + mat_id] = np.full((nsteps,),np.nan,dtype=np.float64)
offset = np.diff(psi_idx)[0]
for i, idx in enumerate(psi_idx):
matrices['psi_' + mat_id][i] = float(f[idx])
temp = f[idx+1:idx+offset]
temp = np.array([str2complex(elem) for elem in temp])
iqty = 0
for jpert in range(0,M):
for ipert in range(0,M):
matrices[mat_id][i,ipert,jpert] = temp[iqty]
iqty +=1
assert not np.any(np.isnan(matrices['psi_' + mat_id]))
assert not np.any(np.isnan(matrices[mat_id]))
idx = np.argsort(matrices['psi_' + mat_id])
matrices['psi_' + mat_id] = matrices['psi_' + mat_id][idx]
matrices[mat_id] = matrices[mat_id][idx]
psis = np.stack([matrices['psi_' + mat_id] for mat_id in 'ABCDEH'])
assert np.allclose(np.std(psis,axis=0),0), "different psi grids!"
fourfit_mats = {mat_id:matrices[mat_id] for mat_id in 'ABCDEH'}
fourfit_mats['psi_grid'] = psis[0]
return fourfit_mats
def read_metric(filename,mpsi,mtheta):
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
f = np.array(f)
metric = np.full((mpsi,mtheta,8),np.nan)
psi_metric = np.full(mpsi,np.nan)
psi_idx = np.arange(0,len(f),8*mtheta+1)
for i, idx in enumerate(psi_idx):
psi_metric[i] = float(f[idx])
for j in range(8):
metric[i,:,j] = np.array([float(foo) for foo in f[idx+mtheta*j+1:idx+mtheta*(j+1)+1]])
assert not np.any(np.isnan(psi_metric))
assert not np.any(np.isnan(metric))
idx = np.argsort(psi_metric)
psi_metric = psi_metric[idx]
metric = metric[idx]
theta_grid = np.linspace(0,1,mtheta)
out_metric = {'psi_grid':psi_metric,
'theta_grid':theta_grid,
'g11':metric[:,:,0],
'g22':metric[:,:,1],
'g33':metric[:,:,2],
'g23':metric[:,:,3],
'g31':metric[:,:,4],
'g12':metric[:,:,5],
'jac':metric[:,:,6],
'jac_prime':metric[:,:,7]}
return out_metric
def read_fourfit_metric(directory,M):
matrices = {}
filenames = ['fourG11.out','fourG22.out','fourG33.out','fourG23.out',
'fourG31.out','fourG12.out','fourjac.out','fourjac1.out']
matnames = ['G11','G22','G33','G23','G31','G12','Jmat','Jmat_prime']
for filename,matname in zip(filenames,matnames):
with open(directory + '/' + filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_idx = np.array([i for i, line in enumerate(f) if '(' not in line])
nsteps = len(psi_idx)
np.testing.assert_almost_equal(np.std(np.diff(psi_idx)),0,err_msg='Unequal matrix sizes at different psi locations!')
offset = np.diff(psi_idx)[0]
M = int(offset/2)
matrices[matname] = np.full((nsteps,M,M),np.nan,dtype=np.complex128)
matrices['psi_' + matname] = np.full((nsteps,),np.nan,dtype=np.float64)
for k, idx in enumerate(psi_idx):
matrices['psi_' + matname][k] = float(f[idx])
temp = f[idx+1:idx+offset]
temp = np.array([str2complex(elem) for elem in temp])
for ii in range(M):
for jj in range(M):
matrices[matname][k,ii,jj] = temp[jj-ii+M-1]
assert not np.any(np.isnan(matrices['psi_' + matname]))
assert not np.any(np.isnan(matrices[matname]))
idx = np.argsort(matrices['psi_' + matname])
matrices['psi_' + matname] = matrices['psi_' + matname][idx]
matrices[matname] = matrices[matname][idx]
psis = np.stack([matrices['psi_' + matname] for matname in matnames])
assert np.allclose(np.std(psis,axis=0),0), "different psi grids!"
fourfit_metric_mats = {matname:matrices[matname] for matname in matnames}
fourfit_metric_mats['psi_grid'] = psis[0]
return fourfit_metric_mats
def readFbarmat(filename,M):
"""Reads bar(F) from text files. Note that bar(F) must be multiplied by Q to get F used in L matrix"""
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_idx = []
for i, line in enumerate(f):
if '(' not in line:
psi_idx.append(i)
psi_idx = np.array(psi_idx)
nsteps = len(psi_idx)
np.testing.assert_almost_equal(np.std(np.diff(psi_idx)),0,err_msg='Unequal matrix sizes at different psi locations!')
psi = np.full((nsteps,),np.nan,dtype=np.float64)
Fdata = np.full((nsteps,M,M),0,dtype=np.complex128)
offset = np.diff(psi_idx)[0]
for i, idx in enumerate(psi_idx):
psi[i] = float(f[idx])
temp = f[idx+1:idx+offset]
temp = np.array([str2complex(elem) for elem in temp])
iqty = 0
for jpert in range(0,M):
for ipert in range(jpert,M):
Fdata[i,ipert,jpert] = temp[iqty]
iqty +=1
# F is stored as lower cholesky factored Fbar, need to square and also multiply by q^2
Fdata[i] = np.matmul(Fdata[i],Fdata[i].conj().T)
assert not np.any(np.isnan(psi))
assert not np.any(np.isnan(Fdata))
Fdata = np.array([(F + F.conj().T)/2 for F in Fdata])
idx = np.argsort(psi)
psi_f = psi[idx]
Fbardata = Fdata[idx]
return psi_f, Fbardata
def readKbarmat(filename,M):
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_idx = []
for i, line in enumerate(f):
if '(' not in line:
psi_idx.append(i)
psi_idx = np.array(psi_idx)
nsteps = len(psi_idx)
np.testing.assert_almost_equal(np.std(np.diff(psi_idx)),0,err_msg='Unequal matrix sizes at different psi locations!')
psi = np.full((nsteps,),np.nan,dtype=np.float64)
Kdata = np.full((nsteps,M,M),np.nan,dtype=np.complex128)
offset = np.diff(psi_idx)[0]
for i, idx in enumerate(psi_idx):
psi[i] = float(f[idx])
temp = f[idx+1:idx+offset]
temp = np.array([str2complex(elem) for elem in temp])
iqty = 0
for jpert in range(0,M):
for ipert in range(0,M):
Kdata[i,ipert,jpert] = temp[iqty]
iqty +=1
assert not np.any(np.isnan(psi))
assert not np.any(np.isnan(Kdata))
idx = np.argsort(psi)
psi_k = psi[idx]
Kbardata = Kdata[idx]
return psi_k, Kbardata
def readGmat(filename,M):
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_idx = []
for i, line in enumerate(f):
if '(' not in line:
psi_idx.append(i)
psi_idx = np.array(psi_idx)
nsteps = len(psi_idx)
np.testing.assert_almost_equal(np.std(np.diff(psi_idx)),0,err_msg='Unequal matrix sizes at different psi locations!')
psi = np.full((nsteps,),np.nan,dtype=np.float64)
Gdata = np.full((nsteps,M,M),np.nan,dtype=np.complex128)
offset = np.diff(psi_idx)[0]
for i, idx in enumerate(psi_idx):
psi[i] = float(f[idx])
temp = f[idx+1:idx+offset]
temp = np.array([str2complex(elem) for elem in temp])
iqty = 0
for jpert in range(0,M):
for ipert in range(jpert,M):
Gdata[i,ipert,jpert] = temp[iqty]
Gdata[i,jpert,ipert] = temp[iqty].conj()
iqty +=1
assert not np.any(np.isnan(psi))
assert not np.any(np.isnan(Gdata))
Gdata = np.array([(G + G.conj().T)/2 for G in Gdata])
idx = np.argsort(psi)
psi_g = psi[idx]
Gdata = Gdata[idx]
return psi_g, Gdata
def readQmat(filename,M):
"""Reads Q = m-nq from text file"""
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_idx = np.arange(len(f))[::M+1]
psi_q = np.full(len(psi_idx),np.nan)
Qdata = np.full((len(psi_idx),M,M),np.nan)
for i, idx in enumerate(psi_idx):
psi_q[i] = float(f[idx])
temp = np.array([float(foo) for foo in f[idx+1:idx+M+1]])
Qdata[i,:,:] = np.diag(temp)
assert not np.any(np.isnan(psi_q))
assert not np.any(np.isnan(Qdata))
idx = np.argsort(psi_q)
psi_q = psi_q[idx]
Qdata = Qdata[idx]
return psi_q, Qdata
def read_coeff_mats(directory,M):
psi_q, Q = readQmat(directory + '/qmat.out',M)
psi_f, Fbar = readFbarmat(directory + '/fmat.out',M)
psi_g, G = readGmat(directory + '/gmat.out',M)
psi_k, Kbar = readKbarmat(directory + '/kmat.out',M)
psis = np.stack([psi_q,psi_f,psi_g,psi_k])
assert np.allclose(np.std(psis,axis=0),0), "different psi grids!"
F = np.matmul(np.matmul(Q,Fbar),Q)
K = np.matmul(Q,Kbar)
coeff_mats = {'psi_grid':psis[0],
'F':F,
'Fbar':Fbar,
'G':G,
'K':K,
'Kbar':Kbar,
'Q':Q}
return coeff_mats
def read_sq_mat(filename):
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
psi_sq = np.array([float(foo) for foo in f[::5]])
F = np.array([float(foo) for foo in f[1::5]])
P = np.array([float(foo) for foo in f[2::5]])
jac = np.array([float(foo) for foo in f[3::5]])
q = np.array([float(foo) for foo in f[4::5]])
sq = {'psi_grid':psi_sq,
'F':F,
'P':P,
'jac':jac,
'q':q}
return sq
def read_rzphi_mat(filename):
with open(filename,'r') as foo:
f = list(foo)
for i, line in enumerate(f):
if isinstance(line,str):
f[i] = line.strip().split()
f = flatten(f)
mpsi = None
mtheta = None
for i, line in enumerate(f):
if float(line) == 0 and mpsi is None:
mpsi = i
if float(line) == 1 and mtheta is None:
mtheta = i-mpsi + 1
psi_grid = np.array([float(foo) for foo in f[:mpsi]])
theta_grid = np.array([float(foo) for foo in f[mpsi:mpsi+mtheta]])
griddata = f[mpsi+mtheta:]
r2 = np.full((mpsi,mtheta),np.nan)
deta = np.full((mpsi,mtheta),np.nan)
dphi = np.full((mpsi,mtheta),np.nan)
jac = np.full((mpsi,mtheta),np.nan)
k = 0
for i in range(mpsi):
for j in range(mtheta):
r2[i,j] = float(griddata[k])
deta[i,j] = float(griddata[k+1])
dphi[i,j] = float(griddata[k+2])
jac[i,j] = float(griddata[k+3])
k += 4
assert not np.any(np.isnan(r2))
assert not np.any(np.isnan(deta))
assert not np.any(np.isnan(dphi))
assert not np.any(np.isnan(jac))
rzphi_arrs = {'psi_grid':psi_grid,
'theta_grid':theta_grid,
'r_squared':r2,
'delta_eta':deta,
'delta_phi':dphi,
'jac':jac}
return rzphi_arrs
def run_stride(gfile, return_WpWv=True, return_metric=True, return_direct=True, return_coeffs=True,
return_interval_details=True, return_timing=True, ninters=50, nthreads=1, verbose=True):
assert os.path.exists('./stride'), "stride program not found in cwd"
dst = 'g'
if os.path.exists(dst):
os.remove(dst)
if isinstance(gfile,str):
gfile_path = gfile
os.symlink(gfile_path, dst)
else:
write_gfile('g',**gfile)
gfile_path = 'g' + str(gfile['shot']) + '.' + str(gfile['time'])
try:
raw_output = subprocess.run(['./stride',str(ninters),str(nthreads)],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True)
except:
raise
if raw_output.returncode != 0:
print('failed for gfile: ',gfile_path)
raise Exception(raw_output.stderr, raw_output.stdout)
elif verbose:
print('run suceeded for gfile: ',gfile_path)
time.sleep(2)
# get locations of singular surfaces, mode numbers, etc
sing, sing_loc, m_grid, mpsi, mtheta, nn, psio, times, interval_details = parse_raw_output(raw_output.stdout,
return_timing,
return_interval_details)
M = len(m_grid)
N = 2*M
data = {'sing': sing,
'sing_loc': sing_loc,
'm_grid': m_grid,
'mpsi':mpsi,
'mtheta':mtheta,
'nn':nn,
'psio': psio,
'M': M,
'N': N}
if return_interval_details:
data.update({'interval_details':interval_details})
if return_timing:
data.update({'times':times})
if return_WpWv:
if os.path.exists('wp.out'):
Wp_dcon = readWmat('wp.out',M)
os.remove('wp.out')
else:
Wp_dcon = None
if os.path.exists('wv.out'):
Wv_dcon = readWmat('wv.out',M)
os.remove('wv.out')
else:
Wv_dcon = None
if os.path.exists('delta_prime.out'):
delta_prime = readWmat('delta_prime.out',2*len(sing))
os.remove('delta_prime.out')
else:
delta_prime = None
data.update({'Wp_dcon': Wp_dcon,
'Wv_dcon': Wv_dcon,
'delta_prime':delta_prime})
if return_coeffs:
if all([os.path.exists(foo + 'mat.out') for foo in 'abcdeh']):
primitive_mats = read_primitive_matrices('./',M)
_ = [os.remove(foo + 'mat.out') for foo in 'abcdeh']
else:
primitive_mats = None
if all([os.path.exists(foo + 'mat.out') for foo in 'fgkq']):
coeff_mats = read_coeff_mats('./',M)
_ = [os.remove(foo + 'mat.out') for foo in 'fgkq']
else:
coeff_mats = None
data.update({'coefficient_matrices':coeff_mats,
'primitive_matrices':primitive_mats})
if return_metric:
if all([os.path.exists('four' + foo + '.out') for foo in [
'G11','G22','G33','G23','G31','G12','jac','jac1']]):
fourfit_metric = read_fourfit_metric('./',M)
_ = [os.remove('four' + foo + '.out') for foo in [
'G11','G22','G33','G23','G31','G12','jac','jac1']]
else:
fourfit_metric = None
if os.path.exists('metric.out'):
metric = read_metric('metric.out',mpsi+1,mtheta+1)
os.remove("metric.out")
else:
metric = None
data.update({'fourfit_metric':fourfit_metric,
'metric':metric})
if return_direct:
if os.path.exists('sqmat.out'):
profiles = read_sq_mat('sqmat.out')
os.remove('sqmat.out')
else:
profiles = None
if os.path.exists('rzphimat.out'):
rzphi = read_rzphi_mat('rzphimat.out')
os.remove('rzphimat.out')
else:
rzphi = None
data.update({'profiles':profiles,
'straight_field_line_coords':rzphi})
return data