def test_write_splash():
from nexus_base import NexusCore
log = divert_nexus_log()
nc = NexusCore()
assert(not nc.wrote_splash)
nc.write_splash()
assert('Nexus' in log.contents())
assert('Please cite:' in log.contents())
assert(nc.wrote_splash)
restore_nexus_log()
def run_project(self, status=False, status_only=False):
self.log('\nProject starting', n=0)
self.init_cascades()
status_only = status_only or nexus_core.status_only
status = status or status_only or nexus_core.status != nexus_core.status_modes.none
if status:
self.write_simulation_status()
if status_only:
NexusCore.write_end_splash()
return
#end if
#end if
self.log('\nstarting runs:\n' + 30 * '~', n=1)
if nexus_core.dependent_modes <= nexus_core.stages_set:
if nexus_core.monitor:
start_time = time.time()
ipoll = 0
while len(self.progressing_cascades) > 0:
elapsed_time = time.time() - start_time
self.log('elapsed time %.1f s' % elapsed_time,
' memory %3.2f MB' %
(memory.resident(children=True) / 1e6),
n=1,
progress=True)
NexusCore.wrote_something = False
ipoll += 1
self.machine.query_queue()
self.progress_cascades()
self.machine.submit_jobs()
self.update_process_ids()
time.sleep(nexus_core.sleep)
if NexusCore.wrote_something:
self.log()
#end if
#end while
elif len(self.progressing_cascades) > 0:
self.machine.query_queue()
self.progress_cascades()
self.machine.submit_jobs()
self.update_process_ids()
#end if
else:
self.progress_cascades()
#end if
self.log('Project finished\n')
NexusCore.write_end_splash()
def run_project(self,status=False,status_only=False):
self.log('\nProject starting',n=0)
self.init_cascades()
status_only = status_only or nexus_core.status_only
status = status or status_only
if status:
self.write_simulation_status()
if status_only:
NexusCore.write_end_splash()
return
#end if
#end if
self.log('\nstarting runs:\n'+30*'~',n=1)
if nexus_core.dependent_modes <= nexus_core.stages_set:
if nexus_core.monitor:
ipoll = 0
while len(self.progressing_cascades)>0:
#self.log('poll',ipoll,' memory %3.2f MB'%(memory.resident()/1e6),n=1)
NexusCore.wrote_something = False
ipoll+=1
self.machine.query_queue()
self.progress_cascades()
self.machine.submit_jobs()
self.update_process_ids()
time.sleep(nexus_core.sleep)
if NexusCore.wrote_something:
self.log()
#end if
#end while
elif len(self.progressing_cascades)>0:
self.machine.query_queue()
self.progress_cascades()
self.machine.submit_jobs()
self.update_process_ids()
#end if
else:
self.progress_cascades()
#end if
self.log('Project finished\n')
NexusCore.write_end_splash()
def test_enter_leave():
import os
from nexus_base import NexusCore
tpath = testing.setup_unit_test_output_directory('nexus_base','test_enter_leave')
cwd = os.getcwd()
log = divert_nexus_log()
nc = NexusCore()
nc.enter(tpath)
tcwd = os.getcwd()
assert(tcwd==tpath)
assert('Entering' in log.contents())
assert(tpath in log.contents())
nc.leave()
assert(os.getcwd()==cwd)
restore_nexus_log()
def __call__(self,**kwargs):
NexusCore.write_splash()
self.log('Applying user settings')
# guard against invalid settings
not_allowed = set(kwargs.keys()) - Settings.allowed_vars
if len(not_allowed)>0:
self.error('unrecognized variables provided.\nYou provided: {0}\nAllowed variables are: {1}'.format(sorted(not_allowed),sorted(Settings.allowed_vars)))
#end if
# assign simple variables
for name in Settings.core_assign_vars:
if name in kwargs:
nexus_core[name] = kwargs[name]
#end if
#end for
# assign simple variables
for name in Settings.noncore_assign_vars:
if name in kwargs:
nexus_noncore[name] = kwargs[name]
#end if
#end for
# extract settings based on keyword groups
kw = Settings.kw_set(Settings.nexus_vars ,kwargs)
mach_kw = Settings.kw_set(Settings.machine_vars,kwargs)
gamess_kw = Settings.kw_set(Settings.gamess_vars ,kwargs)
if len(kwargs)>0:
self.error('some settings keywords have not been accounted for\nleftover keywords: {0}\nthis is a developer error'.format(sorted(kwargs.keys())))
#end if
# copy input settings
self.transfer_from(mach_kw.copy())
self.transfer_from(gamess_kw.copy())
# process machine settings
self.process_machine_settings(mach_kw)
# process nexus core settings
self.process_core_settings(kw)
# process nexus noncore settings
self.process_noncore_settings(kw)
# transfer select core data to the global namespace
nexus_core_noncore.transfer_from(nexus_core,nexus_core_noncore.keys())
nexus_noncore.set(**nexus_core_noncore.copy()) # prevent write to core namespace
# copy final core and noncore settings
self.transfer_from(nexus_core.copy())
self.transfer_from(nexus_noncore.copy())
# process gamess settings
Gamess.settings(**gamess_kw)
return
def error(self,message,header='settings',exit=True,trace=True):
NexusCore.error(self,message,header,exit,trace)
def __call__(self, **kwargs):
NexusCore.write_splash()
self.log('Applying user settings')
# guard against invalid settings
not_allowed = set(kwargs.keys()) - Settings.allowed_vars
if len(not_allowed) > 0:
self.error(
'unrecognized variables provided\nyou provided: {0}\nallowed variables are: {1}'
.format(sorted(not_allowed), sorted(Settings.allowed_vars)))
#end if
# assign simple variables
for name in Settings.core_assign_vars:
if name in kwargs:
nexus_core[name] = kwargs[name]
#end if
#end for
# assign simple variables
for name in Settings.noncore_assign_vars:
if name in kwargs:
nexus_noncore[name] = kwargs[name]
#end if
#end for
# extract settings based on keyword groups
kw = Settings.kw_set(Settings.nexus_vars, kwargs)
mach_kw = Settings.kw_set(Settings.machine_vars, kwargs)
gamess_kw = Settings.kw_set(Settings.gamess_vars, kwargs)
pwscf_kw = Settings.kw_set(Settings.pwscf_vars, kwargs)
if len(kwargs) > 0:
self.error(
'some settings keywords have not been accounted for\nleftover keywords: {0}\nthis is a developer error'
.format(sorted(kwargs.keys())))
#end if
# copy input settings
self.transfer_from(mach_kw.copy())
self.transfer_from(gamess_kw.copy())
self.transfer_from(pwscf_kw.copy())
# process machine settings
self.process_machine_settings(mach_kw)
# process nexus core settings
self.process_core_settings(kw)
# process nexus noncore settings
self.process_noncore_settings(kw)
# transfer select core data to the global namespace
nexus_core_noncore.transfer_from(nexus_core, nexus_core_noncore.keys())
nexus_noncore.set(
**nexus_core_noncore.copy()) # prevent write to core namespace
# copy final core and noncore settings
self.transfer_from(nexus_core.copy())
self.transfer_from(nexus_noncore.copy())
# process gamess settings
Gamess.settings(**gamess_kw)
# process pwscf settings
Pwscf.settings(**pwscf_kw)
return
def error(self, message, header='settings', exit=True, trace=True):
NexusCore.error(self, message, header, exit, trace)
def test_empty_init():
from nexus_base import NexusCore
nc = NexusCore()
def __call__(self, **kwargs):
kwargs = obj(**kwargs)
# guard against invalid settings
not_allowed = set(kwargs.keys()) - Settings.allowed_vars
if len(not_allowed) > 0:
self.error(
'unrecognized variables provided\nyou provided: {0}\nallowed variables are: {1}'
.format(sorted(not_allowed), sorted(Settings.allowed_vars)))
#end if
# restore default core default settings
restore_nexus_core_defaults()
# process command line inputs, if any
if 'command_line' in kwargs:
nexus_core.command_line = kwargs.command_line
#end if
if nexus_core.command_line:
self.process_command_line_settings(kwargs)
#end if
NexusCore.write_splash()
# print version information
try:
from versions import versions
if versions is not None:
err, s, serr = versions.check(write=False, full=True)
self.log(s)
#end if
except Exception:
None
#end try
self.log('Applying user settings')
# assign simple variables
for name in Settings.core_assign_vars:
if name in kwargs:
nexus_core[name] = kwargs[name]
#end if
#end for
# assign simple variables
for name in Settings.noncore_assign_vars:
if name in kwargs:
nexus_noncore[name] = kwargs[name]
#end if
#end for
# extract settings based on keyword groups
kw = Settings.kw_set(Settings.nexus_vars, kwargs)
mach_kw = Settings.kw_set(Settings.machine_vars, kwargs)
gamess_kw = Settings.kw_set(Settings.gamess_vars, kwargs)
pwscf_kw = Settings.kw_set(Settings.pwscf_vars, kwargs)
qm_pkg_kw = Settings.kw_set(Settings.qm_package_vars, kwargs)
if len(kwargs) > 0:
self.error(
'some settings keywords have not been accounted for\nleftover keywords: {0}\nthis is a developer error'
.format(sorted(kwargs.keys())))
#end if
# copy input settings
self.transfer_from(mach_kw.copy())
self.transfer_from(gamess_kw.copy())
self.transfer_from(pwscf_kw.copy())
# process machine settings
self.process_machine_settings(mach_kw)
# process nexus core settings
self.process_core_settings(kw)
# process nexus noncore settings
self.process_noncore_settings(kw)
# transfer select core data to the global namespace
nexus_core_noncore.transfer_from(nexus_core,
list(nexus_core_noncore.keys()))
nexus_noncore.set(
**nexus_core_noncore.copy()) # prevent write to core namespace
# copy final core and noncore settings
self.transfer_from(nexus_core.copy())
self.transfer_from(nexus_noncore.copy())
# process gamess settings
Gamess.restore_default_settings()
Gamess.settings(**gamess_kw)
# process pwscf settings
Pwscf.restore_default_settings()
Pwscf.settings(**pwscf_kw)
# process quantum package settings
QuantumPackage.restore_default_settings()
QuantumPackage.settings(**qm_pkg_kw)
return