def test_vacf_methods():
import numpy as np
import math
from pwtools import pydos
def assrt(a, b):
np.testing.assert_array_almost_equal(a, b)
# random velocity array: 10 atoms, 50 steps, 50 x (10,3) arrays
a = np.random.rand(50, 10, 3) + 1.0
# random mass vector
m = np.random.rand(10) * 10.0 + 1.0
p1 = pydos.pyvacf(a, method=1)
p2 = pydos.pyvacf(a, method=2)
p3 = pydos.pyvacf(a, method=3)
p1m = pydos.pyvacf(a, method=1, m=m)
p2m = pydos.pyvacf(a, method=2, m=m)
p3m = pydos.pyvacf(a, method=3, m=m)
assrt(p1, p2)
assrt(p1, p3)
assrt(p2, p3)
assrt(p1m, p2m)
assrt(p1m, p3m)
assrt(p2m, p3m)
f1 = pydos.fvacf(a, method=1)
f2 = pydos.fvacf(a, method=2)
f1m = pydos.fvacf(a, method=1, m=m)
f2m = pydos.fvacf(a, method=2, m=m)
assrt(f1, f2)
assrt(f1m, f2m)
assrt(p1, f1)
assrt(p2, f1)
assrt(p3, f1)
assrt(p1, f2)
assrt(p2, f2)
assrt(p3, f2)
assrt(p1m, f1m)
assrt(p2m, f1m)
assrt(p3m, f1m)
assrt(p1m, f2m)
assrt(p2m, f2m)
assrt(p3m, f2m)
def test_vacf_methods():
import numpy as np
import math
from pwtools import pydos
def assrt(a, b):
np.testing.assert_array_almost_equal(a,b)
# random velocity array: 10 atoms, 50 steps, 50 x (10,3) arrays
a = np.random.rand(50,10,3) + 1.0
# random mass vector
m = np.random.rand(10) * 10.0 + 1.0
p1 = pydos.pyvacf(a, method=1)
p2 = pydos.pyvacf(a, method=2)
p3 = pydos.pyvacf(a, method=3)
p1m = pydos.pyvacf(a, method=1, m=m)
p2m = pydos.pyvacf(a, method=2, m=m)
p3m = pydos.pyvacf(a, method=3, m=m)
assrt(p1, p2)
assrt(p1, p3)
assrt(p2, p3)
assrt(p1m, p2m)
assrt(p1m, p3m)
assrt(p2m, p3m)
f1 = pydos.fvacf(a, method=1)
f2 = pydos.fvacf(a, method=2)
f1m = pydos.fvacf(a, method=1, m=m)
f2m = pydos.fvacf(a, method=2, m=m)
assrt(f1, f2)
assrt(f1m, f2m)
assrt(p1, f1)
assrt(p2, f1)
assrt(p3, f1)
assrt(p1, f2)
assrt(p2, f2)
assrt(p3, f2)
assrt(p1m, f1m)
assrt(p2m, f1m)
assrt(p3m, f1m)
assrt(p1m, f2m)
assrt(p2m, f2m)
assrt(p3m, f2m)
def test_f2py_flib_openmp():
import numpy as np
from pwtools import _flib
from pwtools.pydos import fvacf
from pwtools.common import backtick
import os
import sys
OMP_DCT = {'num_threads': None}
def omp_num_threads(action='check', num=1, omp_dct=OMP_DCT, err=False):
key = 'OMP_NUM_THREADS'
has_key = key in os.environ
if action == 'check':
if has_key:
print("[omp_num_threads] os.environ['%s']: %s" %
(key, os.environ[key]))
print("[omp_num_threads] shell$ echo %s" % (key))
print(backtick('echo $%s' % key))
if err and os.environ[key] != '3':
return 'err'
else:
print("[omp_num_threads] no os.environ['%s']" % key)
if err:
return 'err'
elif action == 'backup':
if has_key:
print("[omp_num_threads] backup os.environ['%s'] = '%s'" %
(key, os.environ[key]))
omp_dct['num_threads'] = os.environ[key]
else:
omp_dct['num_threads'] = None
elif action == 'restore':
if has_key:
print("[omp_num_threads] restoring os.environ['%s'] = '%s'" \
%(key, omp_dct['num_threads']))
os.environ[key] = omp_dct['num_threads']
elif action == 'set':
print("[omp_num_threads] setting os.environ['%s'] = '%s'" %
(key, str(num)))
os.environ[key] = str(num)
rand = np.random.rand
nat = 10
nstep = 500
vel = rand(nstep, nat, 3)
mass = rand(nat)
cc = np.zeros((nstep, ))
bar = '-' * 70
ret = omp_num_threads('check', err=True)
if ret == 'err':
print(bar)
print("""Do
$ export OMP_NUM_THREADS=3
before running this test.""")
print(bar + '\n')
sys.exit(0)
omp_num_threads('check')
omp_num_threads('backup')
omp_num_threads('set', num=4)
#-----------------------------------------------------------------------------
print(bar)
print(
"""testing _flib.vacf(vel,mass,cc,1,1), no nthreads from Python -- extension
called directly ... does NOT read os.environ, reacts only if OMP_NUM_THREADS
has been set in the shell BEFORE this test script was called""")
omp_num_threads('check')
cc = _flib.vacf(vel, mass, cc, 1, 1)
print(bar + '\n')
#-----------------------------------------------------------------------------
print(bar)
nthreads = 2
print(
"testing _flib.vacf(vel,mass,cc,1,1,nthreads), setting nthreads = %i" %
nthreads)
cc = _flib.vacf(vel, mass, cc, 1, 1, nthreads)
print(bar + '\n')
#-----------------------------------------------------------------------------
print(bar)
print(
"testing _flib.vacf(vel,mass,cc,1,1), no nthreads from Python, take two"
)
print("*" * 70)
print("""!!! POSSIBLE F2PY BUG !!!
After calling omp_set_num_threads() in the last test, OMP_NUM_THREADS is no
longer recognized on the Fortran side!!! nthreads is still at the value from
the last test: %s, that is WRONG
!!! POSSIBLE F2PY BUG !!!""" % nthreads)
print("*" * 70)
omp_num_threads('check')
cc = _flib.vacf(vel, mass, cc, 1, 1)
print(bar + '\n')
#-----------------------------------------------------------------------------
print(bar)
nthr = 2
print("""testing pydos.fvacf(vel, m=mass, nthreads=%i) --
override any OMP_NUM_THREADS setting in the environment AND os.environ""" %
nthreads)
cc = fvacf(vel, m=mass, nthreads=nthreads)
print(bar + '\n')
#-----------------------------------------------------------------------------
print(bar)
print(
"""testing pydos.fvacf(vel, m=mass, nthreads=None): no nthreads from Python -- It
reads os.environ (workaround for f2py bug).""")
omp_num_threads('check')
cc = fvacf(vel, m=mass, nthreads=None)
print(bar + '\n')
omp_num_threads('restore')
def test_f2py_flib_openmp():
import numpy as np
from pwtools import _flib
from pwtools.pydos import fvacf
from pwtools.common import backtick
import os
import sys
OMP_DCT = {'num_threads': None}
def omp_num_threads(action='check', num=1, omp_dct=OMP_DCT, err=False):
key = 'OMP_NUM_THREADS'
has_key = os.environ.has_key(key)
if action == 'check':
if has_key:
print "[omp_num_threads] os.environ['%s']: %s" %(key, os.environ[key])
print "[omp_num_threads] shell$ echo %s" %(key)
print backtick('echo $%s' %key)
if err and os.environ[key] != '3':
return 'err'
else:
print "[omp_num_threads] no os.environ['%s']" %key
if err:
return 'err'
elif action == 'backup':
if has_key:
print "[omp_num_threads] backup os.environ['%s'] = '%s'" %(key, os.environ[key])
omp_dct['num_threads'] = os.environ[key]
else:
omp_dct['num_threads'] = None
elif action == 'restore':
if has_key:
print "[omp_num_threads] restoring os.environ['%s'] = '%s'" \
%(key, omp_dct['num_threads'])
os.environ[key] = omp_dct['num_threads']
elif action == 'set':
print "[omp_num_threads] setting os.environ['%s'] = '%s'" %(key, str(num))
os.environ[key] = str(num)
rand = np.random.rand
nat = 10
nstep = 500
vel = rand(nstep, nat, 3)
mass = rand(nat)
cc = np.zeros((nstep,))
bar = '-'*70
ret = omp_num_threads('check', err=True)
if ret == 'err':
print bar
print """Do
$ export OMP_NUM_THREADS=3
before running this test."""
print bar + '\n'
sys.exit(0)
omp_num_threads('check')
omp_num_threads('backup')
omp_num_threads('set', num=4)
#-----------------------------------------------------------------------------
print bar
print """testing _flib.vacf(vel,mass,cc,1,1), no nthreads from Python -- extension
called directly ... does NOT read os.environ, reacts only if OMP_NUM_THREADS
has been set in the shell BEFORE this test script was called"""
omp_num_threads('check')
cc = _flib.vacf(vel,mass,cc,1,1)
print bar + '\n'
#-----------------------------------------------------------------------------
print bar
nthreads = 2
print "testing _flib.vacf(vel,mass,cc,1,1,nthreads), setting nthreads = %i" %nthreads
cc = _flib.vacf(vel,mass,cc,1,1,nthreads)
print bar + '\n'
#-----------------------------------------------------------------------------
print bar
print "testing _flib.vacf(vel,mass,cc,1,1), no nthreads from Python, take two"
print "*" * 70
print """!!! POSSIBLE F2PY BUG !!!
After calling omp_set_num_threads() in the last test, OMP_NUM_THREADS is no
longer recognized on the Fortran side!!! nthreads is still at the value from
the last test: %s, that is WRONG
!!! POSSIBLE F2PY BUG !!!""" %nthreads
print "*" * 70
omp_num_threads('check')
cc = _flib.vacf(vel,mass,cc,1,1)
print bar + '\n'
#-----------------------------------------------------------------------------
print bar
nthr = 2
print """testing pydos.fvacf(vel, m=mass, nthreads=%i) --
override any OMP_NUM_THREADS setting in the environment AND os.environ""" %nthreads
cc = fvacf(vel, m=mass, nthreads=nthreads)
print bar + '\n'
#-----------------------------------------------------------------------------
print bar
print """testing pydos.fvacf(vel, m=mass, nthreads=None): no nthreads from Python -- It
reads os.environ (workaround for f2py bug)."""
omp_num_threads('check')
cc = fvacf(vel, m=mass, nthreads=None)
print bar + '\n'
omp_num_threads('restore')