return np.max(np.abs(spec - ref))
def get_stats(calculated, reference):
X = np.abs(calculated - reference)
mean = X.mean()
var = X.var()
return mean, var
# check that a job-name directory exists in the work dir and look for
# configuration there
chkptpath = Path('metacfg.yaml')
if chkptpath.exists():
print('Found checkpoint in `{!s}`'.format(chkptpath))
chkpt = SimulationCheckpoint.from_yaml_file(str(chkptpath))
else:
print('A checkpoint file is required at `{!s}`'.format(str(chkptpath)))
exit(-1)
cfgpath = chkptpath.parent / 'template-cfg.yaml'
if cfgpath.exists():
cfg = pyqcfp.QcfpConfig.from_yaml_file(str(cfgpath))
print('Found template QcfpConfig file')
else:
print('A template QcfpConfig file is required at `{!s}`'.format(
str(cfgpath)))
exit(-1)
# start from scratch
# setup checkpoint
TMPDIR = Path(TMPDIR).absolute()
SCRATCHDIR = Path(SCRATCHDIR).absolute()
OUTPUTDIR = Path(OUTPUTDIR).absolute()
#TMPDIR = PurePosixPath('/dev/shm/simulations/17-03-28/')
#TMPDIR = PurePosixPath('C:/aloukian-project/17-03-22')
#SCRATCHDIR = PurePosixPath('/home/aloukian/simulations/17-03-28/')
#SCRATCHDIR = TMPDIR
#OUTPUTDIR = SCRATCHDIR
print('TMPDIR: ', TMPDIR)
print('SCRATCHDIR: ', SCRATCHDIR)
print('OUTPUTDIR: ', OUTPUTDIR)
metacfg = SimulationCheckpoint()
cfg = QcfpConfig()
# meta info
cfg.simulation_id = 0
cfg.simulation_group = 'Ji-dimer-mu-uncoupled'
cfg.simulation_type = 'pump-probe'
cfg.simulation_code = 'excitons-2d'
#cfg.simulation_type = 'absorption'
#cfg.simulation_code = 'excitons-abs'
cfg.full_output = False
cfg.analytic_orientational_averaging = False
cfg.return_axes = False
metacfg.tmpdir = str(TMPDIR)
metacfg.scratchdir = str(SCRATCHDIR)
def simulate(metacfg_path, templatecfg_path, ncores):
# ------------------------------------------------------------------------------
# Set some params and load configuration options
def calculate_delta_cn(spec, ref):
return np.max(np.abs(spec - ref))
def get_stats(calculated, reference):
X = np.abs(calculated - reference)
mean = X.mean()
var = X.var()
return mean, var
chkptpath = Path(metacfg_path)
cfgpath = Path(templatecfg_path)
if chkptpath.exists():
print('Found checkpoint in `{!s}`'.format(chkptpath))
chkpt = SimulationCheckpoint.from_yaml_file(str(chkptpath))
else:
print('A checkpoint file is required at `{!s}`'.format(str(chkptpath)))
exit(-1)
if cfgpath.exists():
cfg = pyqcfp.QcfpConfig.from_yaml_file(str(cfgpath))
print('Found template QcfpConfig file')
else:
print('A template QcfpConfig file is required at `{!s}`'.format(
str(cfgpath)))
exit(-1)
# start from scratch
#chkpt.randstate = random.getstate()
chkpt.usecheckpoint = False
chkpt.nchunks = 0
# ------------------------------------------------------------------------------
# start creating pipeline
template_gen = CfgIdentity(cfg, count=None)
def set_tmp(cfg):
cfg.output_directory = chkpt.tmpdir
tmp_setter = ApplyLambda(set_tmp)
id_gen = TagId(start_id=0)
lst = [template_gen, tmp_setter]
if chkpt.use_staticdisorder:
disorder_gen = AddIIDStaticDisorder([
stats.norm(mu, sigma)
for mu, sigma in chkpt.static_disorder_musigma
])
lst.append(disorder_gen)
if chkpt.use_rotations:
if chkpt.use_stark:
stark_splitter = StarkSplitter()
lst.append(stark_splitter)
mesh_gen = RotateSDesign(mesh_order=chkpt.mesh_size[0],
nrotations=chkpt.mesh_size[1])
lst.append(mesh_gen)
if chkpt.use_stark: #every npts points, turn on analytic averaging
class PeriodicConfig:
def __init__(self, npts):
self.npts = npts
self._pts_seen = 0
def __call__(self, cfg):
self._pts_seen += 1
if self._pts_seen == (self.npts + 1):
cfg.analytic_orientational_averaging = True
self._pts_seen = 0
return cfg
class SliceCfg:
# throw away remaining points for the analytic averaging
def __init__(self, start, stop, step):
self._start = start
self._stop = stop
self._step = step
def transformed(self, cfg):
for c in islice(cfg, self._start, self._stop, self._step):
yield c
lmb = ApplyLambda(PeriodicConfig(mesh_gen.npts))
sl = SliceCfg(None, mesh_gen.npts + 1,
None) # should probably be a common
# variable
lst.append(lmb)
lst.append(sl)
lst.append(id_gen)
# determine how many points to use when distributing simulation over cluster
if chkpt.use_rotations:
# if using rotations, have to average over the whole mesh
if chkpt.use_stark:
# with stark, we get one mesh for field on and one for field off,
# take them both
pts_to_use = mesh_gen.npts + 1
else:
pts_to_use = mesh_gen.npts
if chkpt.use_staticdisorder:
# if using static disorder, calculate that in outer loop
pts_for_loop = chkpt.chunksize
else:
pts_for_loop = 1
else:
# not using rotational averaging, so we're going to take chunksize points
pts_to_use = chkpt.chunksize
pts_for_loop = 1
# ------------------------------------------------------------------------------
# initialize pool of workers for running qcfp
pool = ProcessPoolExecutor(max_workers=ncores)
# combine the simulation pipeline
make_pipeline = compose_transformations(*lst)
cfg_stream = make_pipeline()
# open a file that the main thread will write to
dstore_name = '{simtype}.h5'.format(simtype=cfg.simulation_type)
datastore = h5py.File(dstore_name, 'w')
# compute a single spectrum to make the *.wrk files
tmp_pipeline = compose_transformations(template_gen, tmp_setter)
reference_cfg = list(toolz.take(1, tmp_pipeline()))[0]
reference_cfg.analytic_orientational_averaging = True
reference_cfg.use_stark = False
reference_cfg.return_axes = True
reference_cfg.full_output = False
future = pool.submit(run_simulation, reference_cfg)
simout = future.result()
# Initialize file based on the first run of the simulator
dsetshape = simout.signal.shape
dsetdtype = simout.signal.dtype
refstore = datastore.create_dataset('reference', data=simout.signal)
datastore.create_dataset('w3', data=simout.w3)
datastore.create_dataset('w1', data=simout.w1)
datastore.create_dataset('cfg', data=cfg.to_yaml())
datastore.create_dataset('chkpt', data=chkpt.to_yaml())
# save the metadata
meta = datastore.create_group('meta')
metadsets = {}
for k, v in simout.metainfo.items():
d = np.array(v)
print(k, d)
meta.create_dataset(k, shape=d.shape, data=d)
metadsets[k] = d.shape, d.dtype
# ------------------------------------------------------------------------------
print('Ran reference simulation. Starting averaging.')
for i in tqdm.trange(pts_for_loop, desc='chunks to run', ncols=100):
grp = datastore.create_group('{:05d}'.format(i))
# setup dataset to write chunks to
shape = (pts_to_use, ) + dsetshape
chunks = (min([pts_for_loop, 100]), ) + dsetshape
dset = grp.create_dataset('data',
shape,
dtype=dsetdtype,
chunks=chunks)
# setup metadata folder
meta = grp.create_group('meta')
for k, (s, dtype) in metadsets.items():
shape = (pts_to_use, ) + s
chunks = (min([pts_for_loop, 100]), ) + s
meta.create_dataset(k,
shape=shape,
dtype=dtype,
chunks=chunks,
compression='gzip',
compression_opts=4,
shuffle=True)
futures = pool.map(run_simulation, toolz.take(pts_to_use, cfg_stream))
for simout in tqdm.tqdm(futures,
desc='rotational averages',
total=pts_to_use,
ncols=100):
idx = simout.id
dset[idx, :] = simout.signal
for k in metadsets.keys():
meta[k][idx, :] = simout.metainfo[k]
# ------------------------------------------------------------------------------
# finished with averaging
datastore.close()
print('Averaging completed.')
