def runMonitorsAtSample(E, m2sout, out):
from mcni.utils.conversion import e2v
v = e2v(E)
from pyre.units.time import second
L = 13.6
t = L/v
neutronfile = os.path.join(m2sout, 'neutrons')
from mcni.neutron_storage.idf_usenumpy import count
n = count(neutronfile)
cmd = ['arcs_analyze_beam']
cmd += ['--output-dir=%s' % out]
cmd += ['--ncount=%s' % n]
cmd += ['--buffer_size=%s' % min(n, 1e6)]
cmd += ['--source.path=%s' % neutronfile]
# fix monitor params that depend on incident energy
cmd += ['--monitor.mtof.tofmin=%s' % (t*0.9)]
cmd += ['--monitor.mtof.tofmax=%s' % (t*1.1)]
cmd += ['--monitor.mtof.ntof=%s' % (1000)]
cmd += ['--monitor.menergy.energymin=%s' % (E*0.9)]
cmd += ['--monitor.menergy.energymax=%s' % (E*1.1)]
cmd += ['--monitor.menergy.nenergy=%s' % (1000)]
cmd = ' '.join(cmd)
print 'Running beam monitors...'
_exec(cmd)
print 'done.'
time.sleep(1)
return
def _normalize(input, N, output):
"""normalize the neutrons in the given file by the factor N
and save it in the output
"""
import os
input = os.path.abspath(input)
output = os.path.abspath(output)
# guards
assert input != output
if os.path.exists(output):
raise IOError('%s already exists' % output)
# total # of neutrons
remain = count(input)
# output storage
out = storage(output, mode='w')
# input storage
input = storage(input)
#
chunk = int(1e6)
#
from mcni import neutron_buffer
nb = neutron_buffer(0)
while remain:
n = min(remain, chunk)
# read
neutrons = input.read(n, asnpyarr=True)
# normalize
neutrons[:, -1] /= N
# write
nb.from_npyarr(neutrons)
out.write(nb)
#
remain -= n
continue
return
def _normalize(input, N, output):
"""normalize the neutrons in the given file by the factor N
and save it in the output
"""
import os
input = os.path.abspath(input)
output = os.path.abspath(output)
# guards
assert input != output
if os.path.exists(output):
raise IOError('%s already exists' % output)
# total # of neutrons
remain = count(input)
# output storage
out = storage(output, mode='w')
# input storage
input = storage(input)
#
chunk = int(1e6)
#
from mcni import neutron_buffer
nb = neutron_buffer(0)
while remain:
n = min(remain, chunk)
# read
neutrons = input.read(n, asnpyarr=True)
# normalize
neutrons[:, -1] /= N
# write
nb.from_npyarr(neutrons)
out.write(nb)
#
remain -= n
continue
return
def runMonitorsAtSample(E, m2sout, out, L=LSAMPLE, instrument='arcs'):
from mcni.utils.conversion import e2v
v = e2v(E)
from pyre.units.time import second
t = L/v
neutronfile = os.path.join(m2sout, 'neutrons')
from mcni.neutron_storage.idf_usenumpy import count
n = count(neutronfile)
cmd = ['mcvine instruments %s analyze_beam' % instrument]
cmd += ['--output-dir=%s' % out]
cmd += ['--ncount=%s' % n]
cmd += ['--buffer_size=%s' % min(n, int(1e6))]
cmd += ['--source.path=%s' % neutronfile]
# fix monitor params that depend on incident energy
cmd += ['--monitor.mtof.tofmin=%s' % (t*0.9)]
cmd += ['--monitor.mtof.tofmax=%s' % (t*1.1)]
cmd += ['--monitor.mtof.ntof=%s' % (1000)]
cmd += ['--monitor.menergy.energymin=%s' % (E*0.9)]
cmd += ['--monitor.menergy.energymax=%s' % (E*1.1)]
cmd += ['--monitor.menergy.nenergy=%s' % (1000)]
cmd = ' '.join(cmd)
print('Running beam monitors...')
_exec(cmd)
print('done.')
time.sleep(1)
return
def runMonitorsAtSample(E, LMS, m2sout, out):
from mcni.utils.conversion import e2v
v = e2v(E)
from pyre.units.time import second
L = LMM + LMS
t = L/v
neutronfile = os.path.join(m2sout, 'neutrons')
from mcni.neutron_storage.idf_usenumpy import count
n = count(neutronfile)
cmd = ['mcvine_analyze_beam']
cmd += ['--output-dir=%s' % out]
cmd += ['--ncount=%s' % n]
cmd += ['--buffer_size=%s' % min(n, 1e6)]
# XXX: -0.15 comes from the fact that the in hyspec_moderator2sample
# XXX: the neutron storage is 0.15 before the sample position
cmd += ['--geometer.source="((0,0,-0.15),(0,0,0))"']
cmd += ['--source.path=%s' % neutronfile]
# fix monitor params that depend on incident energy
cmd += ['--monitor.mtof.tofmin=%s' % (t*0.9)]
cmd += ['--monitor.mtof.tofmax=%s' % (t*1.1)]
cmd += ['--monitor.mtof.ntof=%s' % (1000)]
cmd += ['--monitor.menergy.energymin=%s' % (E*0.9)]
cmd += ['--monitor.menergy.energymax=%s' % (E*1.1)]
cmd += ['--monitor.menergy.nenergy=%s' % (1000)]
cmd = ' '.join(cmd)
print('Running beam monitors...')
_exec(cmd)
print('done.')
time.sleep(1)
return
def sendneutronstodetsys(
neutronfile=None, scattering_rundir=None, nodes=None, ncount=None,
workdir = None, tofbinsize = None, tofmax=None, detsys = None,
z_rotation = None,
):
"""
run a simulation to send neutrons to det system
workdir: directory where the simulation is run
tofmax: unit: second
tofbinsize: unit: microsecond
z_rotation: angle of rotation applied to the detector system around z axis (vertical). unit: degree
"""
# create workdir if it does not exist
if not os.path.exists(workdir):
os.makedirs(workdir)
# number of neutrons scattered
if not neutronfile:
neutronfile = os.path.join(scattering_rundir, 'out', 'scattered-neutrons')
if not ncount:
from mcni.neutron_storage.idf_usenumpy import count
ncount = count(neutronfile)
# create simulation command
cmd_name = 'sd'
sim_cmd = os.path.join(workdir, cmd_name)
open(sim_cmd, 'wt').write(sd_txt)
# build command
cmd = ['python '+cmd_name]
args = {
'source': 'NeutronFromStorage',
'detsys': 'DetectorSystemFromXml',
'output-dir': 'out',
'detsys.tofparams': '0,%s,%s' % (tofmax, 1e-6*tofbinsize,),
'detsys.instrumentxml': detsys,
'detsys.eventsdat': 'events.dat',
'geometer.detsys': '(0,0,0),(0,%s,0)' % (z_rotation or 0,),
'ncount': ncount,
'source.path': neutronfile,
}
if nodes:
from mcni.pyre_support.MpiApplication \
import mpi_launcher_choice as launcher
args['%s.nodes' % launcher] = nodes
cmd += ['--%s=%s' % (k,v) for k,v in args.iteritems()]
cmd = ' '.join(cmd)
run_sh = os.path.join(workdir, 'run.sh')
open(run_sh, 'w').write(cmd+'\n')
execute(cmd, workdir)
# events.dat
outfile = os.path.join(workdir, 'out', 'events.dat')
return outfile
def sendneutronstodetsys(
neutronfile=None,
scattering_rundir=None,
nodes=None,
ncount=None,
workdir=None,
):
"""
run a simulation to send neutrons to det system
workdir: directory where the simulation is run
"""
# create workdir if it does not exist
if not os.path.exists(workdir):
os.makedirs(workdir)
# number of neutrons scattered
if not neutronfile:
neutronfile = os.path.join(scattering_rundir, 'out',
'scattered-neutrons')
if not ncount:
from mcni.neutron_storage.idf_usenumpy import count
ncount = count(neutronfile)
# create simulation command
cmd_name = 'sd'
sim_cmd = os.path.join(workdir, cmd_name)
open(sim_cmd, 'wt').write(sd_txt)
# build command
cmd = ['python ' + cmd_name]
args = {
'source': 'NeutronFromStorage',
'detsys': 'DetectorSystemFromXml',
'output-dir': 'out',
'detsys.tofparams': '0,1.,%s' % (1e-6 * tofbinsize, ),
'detsys.instrumentxml': cncsxml,
'detsys.eventsdat': 'events.dat',
'ncount': ncount,
'source.path': neutronfile,
}
if nodes:
from mcni.pyre_support.MpiApplication \
import mpi_launcher_choice as launcher
args['%s.nodes' % launcher] = nodes
cmd += ['--%s=%s' % (k, v) for k, v in args.items()]
cmd = ' '.join(cmd)
run_sh = os.path.join(workdir, 'run.sh')
open(run_sh, 'w').write(cmd + '\n')
from .utils import execute
execute(cmd, workdir)
# events.dat
outfile = os.path.join(workdir, 'out', 'events.dat')
return outfile
def sendneutronstodetsys(
neutronfile=None, scattering_rundir=None, nodes=None, ncount=None,
workdir = None,
):
"""
run a simulation to send neutrons to det system
workdir: directory where the simulation is run
"""
# create workdir if it does not exist
if not os.path.exists(workdir):
os.makedirs(workdir)
# number of neutrons scattered
if not neutronfile:
neutronfile = os.path.join(scattering_rundir, 'out', 'scattered-neutrons')
if not ncount:
from mcni.neutron_storage.idf_usenumpy import count
ncount = count(neutronfile)
# create simulation command
cmd_name = 'sd'
sim_cmd = os.path.join(workdir, cmd_name)
open(sim_cmd, 'wt').write(sd_txt)
# build command
cmd = ['python '+cmd_name]
args = {
'source': 'NeutronFromStorage',
'detsys': 'DetectorSystemFromXml',
'output-dir': 'out',
'detsys.tofparams': '0,0.02,%s' % (1e-6*tofbinsize,),
'detsys.instrumentxml': arcsxml,
'detsys.eventsdat': 'events.dat',
'ncount': ncount,
'source.path': neutronfile,
}
if nodes:
from mcni.pyre_support.MpiApplication \
import mpi_launcher_choice as launcher
args['%s.nodes' % launcher] = nodes
cmd += ['--%s=%s' % (k,v) for k,v in args.iteritems()]
cmd = ' '.join(cmd)
run_sh = os.path.join(workdir, 'run.sh')
open(run_sh, 'w').write(cmd+'\n')
from .utils import execute
execute(cmd, workdir)
# events.dat
outfile = os.path.join(workdir, 'out', 'events.dat')
return outfile
def computeFlux(m2sout):
f = os.path.join(m2sout, 'neutrons')
from mcni.neutron_storage.idf_usenumpy import totalintensity, count
I = totalintensity(f)
if I == 0:
raise RuntimeError, "There is no neutrons at sample position. Please increase ncount"
# one MC run corresponds to 34kJ/pulse
# this is the flux if the power is at 34kJ/pulse
# unit: 1/34kJ pulse
# every neutron in the storage represents one 34kJ pulse. so
# we need to normalize by number of events in the storage
nevts = count(f)
flux = I/nevts
return flux
def computeFlux(m2sout):
f = os.path.join(m2sout, 'neutrons')
from mcni.neutron_storage.idf_usenumpy import totalintensity, count
I = totalintensity(f)
if I == 0:
raise RuntimeError("There is no neutrons at sample position. Please increase ncount")
# one MC run corresponds to 34kJ/pulse
# this is the flux if the power is at 34kJ/pulse
# unit: 1/34kJ pulse
# every neutron in the storage represents one 34kJ pulse. so
# we need to normalize by number of events in the storage
nevts = count(f)
flux = I/nevts
return flux
def runMonitorsAtSample(E, m2sout, out, L):
from mcni.utils.conversion import e2v
v = e2v(E)
from pyre.units.time import second
t = L / v
neutronfile = os.path.abspath(os.path.join(m2sout, 'neutrons'))
from mcni.neutron_storage.idf_usenumpy import count
n = count(neutronfile)
# cmd = ['mcvine instruments %s analyze_beam' % instrument]
app = os.path.join(here, 'dgs_bpp_analyze_beam.py')
# create a temp dir to run the simulation
import tempfile
tmpd = tempfile.mkdtemp()
def copy2tmpd(fn):
src = os.path.join(here, fn)
dest = os.path.join(tmpd, fn)
shutil.copyfile(src, dest)
copy2tmpd('dgs_bpp_analyze_beam.pml')
copy2tmpd('beam_analyzer.odb')
cmd = ['python {}'.format(app)]
cmd += ['--output-dir=%s' % os.path.abspath(out)]
cmd += ['--ncount=%s' % n]
cmd += ['--buffer_size=%s' % min(n, int(1e6))]
cmd += ['--source.path=%s' % neutronfile]
# fix monitor params that depend on incident energy
cmd += ['--monitor.mtof.tofmin=%s' % (t * 0.9)]
cmd += ['--monitor.mtof.tofmax=%s' % (t * 1.1)]
cmd += ['--monitor.mtof.ntof=%s' % (1000)]
cmd += ['--monitor.menergy.energymin=%s' % (E * 0.9)]
cmd += ['--monitor.menergy.energymax=%s' % (E * 1.1)]
cmd += ['--monitor.menergy.nenergy=%s' % (1000)]
cmd = ' '.join(cmd)
print('Running beam monitors...')
from mcvine.run_script import _exec
print(cmd, tmpd)
_exec(cmd, cwd=tmpd)
print('done.')
time.sleep(1)
# shutil.rmtree(tmpd)
return
def merge_and_normalize(filename, outputs_dir, overwrite_datafiles=True):
"""merge_and_normalize('scattered-neutrons', 'out')
"""
# find all output files
from mcni.components.outputs import n_mcsamples_files, mcs_sum
import glob, os
pattern = os.path.join(outputs_dir, "*", filename)
nsfiles = glob.glob(pattern)
n_mcsamples = n_mcsamples_files(outputs_dir)
assert len(nsfiles) == n_mcsamples, "neutron storage files %s does not match #mcsample files %s" % (
len(nsfiles),
n_mcsamples,
)
if not nsfiles:
return None, None
# output
out = os.path.join(outputs_dir, filename)
if overwrite_datafiles:
if os.path.exists(out):
os.remove(out)
# merge
from mcni.neutron_storage import merge
merge(nsfiles, out)
# number of neutron events totaly in the neutron file
from mcni.neutron_storage.idf_usenumpy import count
nevts = count(out)
# load number_of_mc_samples
mcs = mcs_sum(outputs_dir)
# normalization factor. this is a bit tricky!!!
nfactor = mcs / nevts
# normalize
from mcni.neutron_storage import normalize
normalize(out, nfactor)
return
def runMonitorsAtSample(E, LMS, m2sout, out):
from mcni.utils.conversion import e2v
v = e2v(E)
from pyre.units.time import second
# this is copied from hyspec_moderator2sample.instr
# XXX: duplicate code. will need to change this
# XXX: if the instrument changes.
L1 = 9.93
L2 = 48.0 * 0.501
L3 = 5.0
LMM = L1 + L2 + L3
L = LMM + LMS
t = L / v
neutronfile = os.path.join(m2sout, "neutrons")
from mcni.neutron_storage.idf_usenumpy import count
n = count(neutronfile)
cmd = ["mcvine_analyze_beam"]
cmd += ["--output-dir=%s" % out]
cmd += ["--ncount=%s" % n]
cmd += ["--buffer_size=%s" % min(n, 1e6)]
# XXX: -0.15 comes from the fact that the in hyspec_moderator2sample
# XXX: the neutron storage is 0.15 before the sample position
cmd += ['--geometer.source="((0,0,-0.15),(0,0,0))"']
cmd += ["--source.path=%s" % neutronfile]
# fix monitor params that depend on incident energy
cmd += ["--monitor.mtof.tofmin=%s" % (t * 0.9)]
cmd += ["--monitor.mtof.tofmax=%s" % (t * 1.1)]
cmd += ["--monitor.mtof.ntof=%s" % (1000)]
cmd += ["--monitor.menergy.energymin=%s" % (E * 0.9)]
cmd += ["--monitor.menergy.energymax=%s" % (E * 1.1)]
cmd += ["--monitor.menergy.nenergy=%s" % (1000)]
cmd = " ".join(cmd)
print "Running beam monitors..."
_exec(cmd)
print "done."
time.sleep(1)
return
def sendneutronstodetsys(scattering_rundir, nodes, ncount=None):
import os
if os.path.exists('out'):
raise IOError, "output directory 'out' already exists. Rename or remove it"
# number of neutrons scattered
neutronfile = os.path.join(scattering_rundir, 'out', 'scattered-neutrons')
if not ncount:
from mcni.neutron_storage.idf_usenumpy import count
ncount = count(neutronfile)
# build command
cmd = ['./sd']
args = {
'ncount': ncount,
'mpirun.nodes': nodes,
'source.path': neutronfile,
}
cmd += ['--%s=%s' % (k,v) for k,v in args.iteritems()]
cmd = ' '.join(cmd)
execute(cmd)
return
def _merge_and_normalize(self):
# XXX: should rewrite using mcni.neutron_storage.merge_and_normalize
outdir = self.simulation_context.outputdir
# find all output files
from mcni.components.outputs import n_mcsamples_files, mcs_sum
import glob, os
filename = self.path
pattern = os.path.join(outdir, '*', filename)
nsfiles = glob.glob(pattern)
n_mcsamples = n_mcsamples_files(outdir)
assert len(nsfiles) == n_mcsamples, \
"neutron storage files %s does not match #mcsample files %s" %(
len(nsfiles), n_mcsamples)
if not nsfiles:
return None, None
# output
out = os.path.join(outdir, self.path)
if self.overwrite_datafiles:
if os.path.exists(out):
os.remove(out)
# merge
from mcni.neutron_storage import merge
merge(nsfiles, out)
# number of neutron events totaly in the neutron file
from mcni.neutron_storage.idf_usenumpy import count
nevts = count(out)
# load number_of_mc_samples
mcs = mcs_sum(outdir)
# normalization factor. this is a bit tricky!!!
nfactor = mcs / nevts
# normalize
from mcni.neutron_storage import normalize
normalize(out, nfactor)
return
def _merge_and_normalize(self):
# XXX: should rewrite using mcni.neutron_storage.merge_and_normalize
outdir = self.simulation_context.outputdir
# find all output files
from mcni.components.outputs import n_mcsamples_files, mcs_sum
import glob, os
filename = self.path
pattern = os.path.join(outdir, '*', filename)
nsfiles = glob.glob(pattern)
n_mcsamples = n_mcsamples_files(outdir)
assert len(nsfiles) == n_mcsamples, \
"neutron storage files %s does not match #mcsample files %s" %(
len(nsfiles), n_mcsamples)
if not nsfiles:
return None, None
# output
out = os.path.join(outdir, self.path)
if self.overwrite_datafiles:
if os.path.exists(out):
os.remove(out)
# merge
from mcni.neutron_storage import merge
merge(nsfiles, out)
# number of neutron events totaly in the neutron file
from mcni.neutron_storage.idf_usenumpy import count
nevts = count(out)
# load number_of_mc_samples
mcs = mcs_sum(outdir)
# normalization factor. this is a bit tricky!!!
nfactor = mcs/nevts
# normalize
from mcni.neutron_storage import normalize
normalize(out, nfactor)
return
def merge_and_normalize(filename, outputs_dir, overwrite_datafiles=True):
"""merge_and_normalize('scattered-neutrons', 'out')
"""
# find all output files
from mcni.components.outputs import n_mcsamples_files, mcs_sum
import glob, os
pattern = os.path.join(outputs_dir, '*', filename)
nsfiles = glob.glob(pattern)
n_mcsamples = n_mcsamples_files(outputs_dir)
assert len(nsfiles) == n_mcsamples, \
"neutron storage files %s does not match #mcsample files %s" %(
len(nsfiles), n_mcsamples)
if not nsfiles:
return None, None
# output
out = os.path.join(outputs_dir, filename)
if overwrite_datafiles:
if os.path.exists(out):
os.remove(out)
# merge
from mcni.neutron_storage import merge
merge(nsfiles, out)
# number of neutron events totaly in the neutron file
from mcni.neutron_storage.idf_usenumpy import count
nevts = count(out)
# load number_of_mc_samples
mcs = mcs_sum(outputs_dir)
# normalization factor. this is a bit tricky!!!
nfactor = mcs / nevts
# normalize
from mcni.neutron_storage import normalize
normalize(out, nfactor)
return
def collimator_inefficiency(self, params):
dcs, I_d, error = self.diffraction_pattern_calculation(params)
scattered = os.path.join(beam_path, 'clampcellSi_neutron')
ncount = 1e9
sample_peaks = self.peaks['sample']
cell_peaks = self.peaks['cell']
scattered_beam_intensity = totalintensity(scattered) * ncount / count(
scattered)
sample_peak_int = 0.0
cell_peak_int = 0.0
for sample_peak in sample_peaks:
sample_peak_int += I_d[(dcs < sample_peak.dmax)
& (dcs > sample_peak.dmin)].sum(
) #I_d[ (dcs<3.5) & (dcs>3)].sum()
for cell_peak in cell_peaks:
cell_peak_int += I_d[(dcs < cell_peak.dmax)
& (dcs > cell_peak.dmin)].sum(
) #I_d[np.logical_and(dcs<2.2, dcs>2)].sum()
# collimator_ineff=(cell_peak_int/sample_peak_int)+(1-sample_peak_int/scattered_beam_intensity)
collimator_ineff = (cell_peak_int / sample_peak_int
) # new objective function suggested by Garrett
print('coll_len,:', params[0], 'focal_distance,:', params[1],
'collimator_performance: ', (sample_peak_int / cell_peak_int))
return (collimator_ineff)
from collimator_geometry import create as create_collimator_geometry, Parameter_error
import reduction, conf
scattered = os.path.join(
beam_path, 'clampcellSi_neutron'
) # path to scattered neutrons from clamp cell and sample
sample = 'collimator'
ncount = 1e5
nodes = 20
sourceTosample = 0
detector_size = 0.5
instr = os.path.join(libpath, 'myinstrument.py')
scattered_beam_intensity = totalintensity(scattered) * ncount / count(
scattered)
samplepath = os.path.join(thisdir, '../sample')
filename = 'coll_geometry.xml'
outputfile = os.path.join(samplepath, filename)
def objective_func(params):
try:
diffraction_pattern = diffraction_pattern_calculation(params)
return (collimator_inefficiency(diffraction_pattern))
except Parameter_error as e:
return (1e10)
def run(beam_neutrons_path, instrument, samplexmlpath, psi, hkl2Q, pixel, t_m2p,
Q, E, hkl_projection, Nbuffer=100000, Nrounds_beam=1):
"""Run mcvine simulation with using the resolution sample and the resolution pixel,
and save the results as numpy arrays
- beam_neutrons_path: path to the "neutrons" file of a beam simulation
- instrument: instrument object with geometry data such as L1 and L2
- samplexmlpath: path to the sampleassembly xml file
- psi: sample rotation angle
- hkl2Q: matrix to convert hkl to Q: Q = hkl dot hkl2Q
- pixel: pixel object with pixe, height, pressure. and position
- t_m2p: exepcted tof from moderator to pixel
- Q: expected Q
- E: expected E
- hkl_projection: the simulated data is projected to this axis and E axis for easy inspection
- Nbuffer: neutron buffer size
- Nrounds_beam: number of rounds replaying neutrons in the beam
"""
from mcni.components.NeutronFromStorage import NeutronFromStorage
source = NeutronFromStorage('source', path=beam_neutrons_path)
from mccomponents.sample import samplecomponent
sample = samplecomponent( 'sample', samplexmlpath)
# dummy component to save the state of scattered neutrons
from mcni.components.Dummy import Dummy
sample_location = Dummy('sample_location')
# det pixel
from mccomponents.components.DGSSXResPixel import DGSSXResPixel
pressure = mcvine.units.parse(pixel.pressure)/mcvine.units.parse("kg/m/s/s")
r = mcvine.units.parse(pixel.radius)/mcvine.units.meter
h = mcvine.units.parse(pixel.height)/mcvine.units.meter
pixel_comp = DGSSXResPixel(
"pixel",
pressure=pressure, tof=t_m2p,
radius=r, height=h)
# build instrument simulation chain
import mcni
sim_chain = mcni.instrument( [source, sample, sample_location, pixel_comp] )
# put components into place
geometer = mcni.geometer()
z_beam = mcvine.units.parse(instrument.offset_sample2beam)/mcvine.units.meter
# z along beam
geometer.register( source, (0,0,z_beam), (0,0,0) )
geometer.register( sample, (0,0,0), (0,psi*180/np.pi,0) )
geometer.register( sample_location, (0,0,0), (0,0,0) )
geometer.register( pixel_comp, pixel.position, pixel.orientation )
#
Q2hkl = np.linalg.inv(hkl2Q)
# lengh of hkl_projection squared
hkl_proj_len2 = np.dot(hkl_projection, hkl_projection)
# neutron buffer
from mcni.neutron_storage.idf_usenumpy import count
N0 = count(beam_neutrons_path) * Nrounds_beam
dxs_all = None; dEs_all = None; probs_all=None; dhkls_all=None
start = 0
for i in range(int(np.ceil(N0/Nbuffer))+1):
# for i in range(10):
end = start + Nbuffer
end = min(end, N0)
if end<=start:
continue
sys.stdout.write("%s-%s: " % (start, end-1)); sys.stdout.flush()
neutrons = mcni.neutron_buffer(end-start)
# simulate
tracer = NeutronTracer()
mcni.simulate( sim_chain, geometer, neutrons, tracer=tracer)
#
before_dummy_start, after_dummy_start, \
before_incident, after_incident, \
before_scattered, after_scattered, \
at_sample_location, at_sample_location2, \
before_detected, after_detected, \
before_dummy_end, after_dummy_end = tracer._store
incident = after_incident
# has to be `at_sample_location` because both sample_location and
# beam have no relative rotation.
# should not used after_scattered.
# it is in the sample's coordinate system, which is rotated by angle psi.
# should not use before_detected. It could be rotated in spherical case
scattered = at_sample_location
detected = after_detected
del (before_dummy_start, after_dummy_start,
before_incident, after_incident,
before_scattered, after_scattered,
before_detected, after_detected,
before_dummy_end, after_dummy_end)
is_scattered = incident.v != scattered.v
is_scattered = np.logical_or(
is_scattered[:,0],
np.logical_or(is_scattered[:,1], is_scattered[:,2])
)
good = np.logical_and(is_scattered, detected.p>np.finfo(float).eps)
vi = incident.v[good]
vf = scattered.v[good]
probs = p = detected.p[good]
from mcni.utils import conversion
Ei = conversion.VS2E * (vi*vi).sum(axis=-1)
Ef = conversion.VS2E * (vf*vf).sum(axis=-1)
Es = Ei - Ef
vQ = vi-vf
Qs = vQ * conversion.V2K
Qs = np.array([Qs[:, 2], Qs[:, 0], Qs[:, 1]]).T
# print Qs
# print Es
dQs = Qs - Q
dEs = Es - E
dhkls = np.dot(dQs, Q2hkl)
# print dhkls
# print dEs
# print p
dxs = np.dot( dhkls, np.array(hkl_projection) )/hkl_proj_len2
if dxs_all is None:
dxs_all = dxs
dEs_all = dEs
probs_all = probs
dhkls_all = dhkls
else:
dxs_all = np.concatenate((dxs_all, dxs))
dEs_all = np.concatenate((dEs_all, dEs))
probs_all = np.concatenate((probs_all, probs))
dhkls_all = np.concatenate((dhkls_all, dhkls))
print()
start = end
continue
# reverse x and E
# the negative sign here makes the result the PSF
dxs_all *= -1
dEs_all *= -1
dhkls_all *= -1
# save results
np.save("dhkls.npy", dhkls_all)
np.save("dxs.npy", dxs_all)
np.save("dEs.npy", dEs_all)
np.save("probs.npy", probs_all)
h, xedges, yedges = np.histogram2d(
dxs_all, dEs_all, bins=100, weights=probs_all)
import histogram as H, histogram.hdf as hh
xaxis = H.axis('x', boundaries=xedges)
Eaxis = H.axis('E', boundaries=yedges)
res = H.histogram('res', (xaxis, Eaxis), data=h)
hh.dump(res, 'res.h5')
sys.stdout.write("Done.\n"); sys.stdout.flush()
return
def sendneutronstodetsys(
neutronfile=None,
scattering_rundir=None,
nodes=None,
ncount=None,
workdir=None,
tofbinsize=None,
tofmax=None,
detsys=None,
z_rotation=None,
):
"""
run a simulation to send neutrons to det system
workdir: directory where the simulation is run
tofmax: unit: second
tofbinsize: unit: microsecond
z_rotation: angle of rotation applied to the detector system around z axis (vertical). unit: degree
"""
# create workdir if it does not exist
if not os.path.exists(workdir):
os.makedirs(workdir)
# number of neutrons scattered
if not neutronfile:
neutronfile = os.path.join(scattering_rundir, 'out',
'scattered-neutrons')
if not ncount:
from mcni.neutron_storage.idf_usenumpy import count
ncount = count(neutronfile)
# create simulation command
cmd_name = 'sd'
sim_cmd = os.path.join(workdir, cmd_name)
open(sim_cmd, 'wt').write(sd_txt)
# build command
cmd = ['python ' + cmd_name]
args = {
'source': 'NeutronFromStorage',
'detsys': 'DetectorSystemFromXml',
'output-dir': 'out',
'detsys.tofparams': '0,%s,%s' % (
tofmax,
1e-6 * tofbinsize,
),
'detsys.instrumentxml': detsys,
'detsys.eventsdat': 'events.dat',
'geometer.detsys': '(0,0,0),(0,%s,0)' % (z_rotation or 0, ),
'ncount': ncount,
'source.path': neutronfile,
}
if nodes:
args['mpirun.nodes'] = nodes
cmd += ['--%s=%s' % (k, v) for k, v in args.iteritems()]
cmd = ' '.join(cmd)
run_sh = os.path.join(workdir, 'run.sh')
open(run_sh, 'w').write(cmd + '\n')
execute(cmd, workdir)
# events.dat
outfile = os.path.join(workdir, 'out', 'events.dat')
return outfile
def run(Ei,
ncount,
nodes,
moderator_erange=None,
fermichopper=None,
fermi_nu=None,
T0_nu=None,
emission_time=None,
dry_run=False):
fermichopper = fermichopper or "100-1.5-SMI"
emission_time = emission_time or -1
fermi_nu = fermi_nu or 600
T0_nu = T0_nu or 120
# generate configration
cmd = """
arcs-m2s \
--fermi_nu=%(fermi_nu)s \
--T0_nu=%(T0_nu)s \
--E=%(Ei)s \
--emission_time=%(emission_time)s \
--fermi_chopper=%(fermichopper)s \
--- \
-dump-pml
""" % locals()
execute(cmd)
# fine tune configuraiton
cmd = ["arcs_moderator2sample --overwrite-datafiles"]
Emin, Emax = moderator_erange
cmd.append('--moderator.Emin=%s' % Emin)
cmd.append('--moderator.Emax=%s' % Emax)
cmd.append("--dump-pml")
cmd = ' '.join(cmd)
execute(cmd)
# run simulation
import os, shutil
if os.path.exists('out'):
shutil.rmtree('out')
cmd = "arcs_moderator2sample -ncount=%(ncount)s " % locals()
# ... moderator data file
moddat = os.path.join(
os.environ['MCVINE_DIR'],
'share',
'mcvine',
'instruments',
'ARCS',
'source_sct521_bu_17_1.dat',
)
cmd += ' -moderator.S_filename=%s ' % moddat
cmd += ' -mpirun.nodes=%s' % nodes
cmd += '> m2s.log 2> m2s.err'
if dry_run:
print cmd
else:
execute(cmd)
# analyze output
# ... number of neutrons left
neutronfile = os.path.join('out', 'neutrons')
from mcni.neutron_storage.idf_usenumpy import count
if dry_run:
ncountatsample = 1000
else:
ncountatsample = count(neutronfile)
if ncountatsample == 0:
raise RuntimeError, "no neutrons at sample. need to increase mc samples at mod2sample simulation"
cmd = [
'arcs_analyze_beam',
'-source.path=%(neutronfile)s' % locals(),
'-ncount=%(ncountatsample)s' % locals(),
'--output-dir=out-analyzer',
]
# ... compute enegy range
from mcni.utils.conversion import e2v
v = e2v(Ei)
from pyre.units.time import second
L = 13.6
t = L / v
# ... build command line with monitor parameters
cmd += ['--monitor.mtof.tofmin=%s' % (t * 0.9)]
cmd += ['--monitor.mtof.tofmax=%s' % (t * 1.1)]
cmd += ['--monitor.mtof.ntof=%s' % (1000)]
cmd += ['--monitor.menergy.energymin=%s' % (Ei * 0.9)]
cmd += ['--monitor.menergy.energymax=%s' % (Ei * 1.1)]
cmd += ['--monitor.menergy.nenergy=%s' % (1000)]
# ... run
cmd = ' '.join(cmd)
if dry_run:
print cmd
else:
execute(cmd)
return
#!/usr/bin/env python
import os
here = os.path.dirname(__file__) or '.'
here = os.path.abspath(here)
scattered = os.path.join(here, '../sample/out/scattered.mcvine')
from mcni.neutron_storage.idf_usenumpy import count
N = count(scattered)
from mcvine import run_script
run_script.run_mpi('./sd.py', 'out', ncount=N, nodes=8, overwrite_datafiles=True)
def run(Ei, ncount, nodes,
moderator_erange = None,
fermichopper=None, fermi_nu=None,
T0_nu = None,
emission_time = None,
dry_run=False):
fermichopper = fermichopper or "100-1.5-SMI"
emission_time = emission_time or -1
fermi_nu = fermi_nu or 600
T0_nu = T0_nu or 120
# generate configration
cmd = """
arcs-m2s \
--fermi_nu=%(fermi_nu)s \
--T0_nu=%(T0_nu)s \
--E=%(Ei)s \
--emission_time=%(emission_time)s \
--fermi_chopper=%(fermichopper)s \
--- \
-dump-pml
""" % locals()
execute(cmd)
# fine tune configuraiton
cmd = ["arcs_moderator2sample --overwrite-datafiles"]
Emin, Emax = moderator_erange
cmd.append('--moderator.Emin=%s' % Emin)
cmd.append('--moderator.Emax=%s' % Emax)
cmd.append("--dump-pml")
cmd = ' '.join(cmd)
execute(cmd)
# run simulation
import os, shutil
if os.path.exists('out'):
shutil.rmtree('out')
cmd = "arcs_moderator2sample -ncount=%(ncount)s " % locals()
# ... moderator data file
moddat = os.path.join(
os.environ['MCVINE_DIR'], 'share', 'mcvine',
'instruments', 'ARCS', 'source_sct521_bu_17_1.dat',
)
cmd += ' -moderator.S_filename=%s ' % moddat
cmd += ' -mpirun.nodes=%s' % nodes
cmd += '> m2s.log 2> m2s.err'
if dry_run:
print cmd
else:
execute(cmd)
# analyze output
# ... number of neutrons left
neutronfile = os.path.join('out', 'neutrons')
from mcni.neutron_storage.idf_usenumpy import count
if dry_run:
ncountatsample = 1000
else:
ncountatsample = count(neutronfile)
if ncountatsample == 0:
raise RuntimeError, "no neutrons at sample. need to increase mc samples at mod2sample simulation"
cmd = [
'arcs_analyze_beam',
'-source.path=%(neutronfile)s' % locals(),
'-ncount=%(ncountatsample)s' % locals(),
'--output-dir=out-analyzer',
]
# ... compute enegy range
from mcni.utils.conversion import e2v
v = e2v(Ei)
from pyre.units.time import second
L = 13.6
t = L/v
# ... build command line with monitor parameters
cmd += ['--monitor.mtof.tofmin=%s' % (t*0.9)]
cmd += ['--monitor.mtof.tofmax=%s' % (t*1.1)]
cmd += ['--monitor.mtof.ntof=%s' % (1000)]
cmd += ['--monitor.menergy.energymin=%s' % (Ei*0.9)]
cmd += ['--monitor.menergy.energymax=%s' % (Ei*1.1)]
cmd += ['--monitor.menergy.nenergy=%s' % (1000)]
# ... run
cmd = ' '.join(cmd)
if dry_run:
print cmd
else:
execute(cmd)
return
