def run_simulation(run_name, dir_path, path_to_working_dir, num_time_steps,
num_outputs):
print("Deleting any pre-existing results...")
# Delete any pre-existing executables or results
if os.path.exists(str(path_to_working_dir) + '/' + run_name) is True:
shutil.rmtree(str(path_to_working_dir) + '/' + run_name)
# Open file where output is redirected to
if os.path.exists(str(path_to_working_dir) + "/output.txt") is True:
os.remove(str(path_to_working_dir) + "/output.txt")
f = open(str(path_to_working_dir) + "/output.txt", 'w+')
for vtu_file in glob.glob(str(path_to_working_dir) + "/*.vtu"):
os.remove(vtu_file)
#shutil.copyfile(dir_path + "../bin", str(path_to_working_dir) + '/bin')
print("Completed")
# Run the simulation
rappture_path = os.path.dirname(os.path.realpath(__file__))
#os.chdir(dir_path)
os.chdir(path_to_working_dir)
print("Running the PRISMS-PF executable...")
exitStatus, stdOutput, stdError = RapptureExec([
"submit", "--local", "--metrics", dir_path + "../bin/main", "-i",
str(path_to_working_dir) + "/parameters_rappture.in"
],
streamOutput=True)
print("Completed with exit status:", exitStatus)
#exitStatus,stdOutput,stdError = RapptureExec(["submit", "--local", "--metrics", dir_path + "../bin/main", "-i", str(path_to_working_dir) + "/parameters_rappture.in"], streamOutput=True)
#fts = open("run_info.txt",'w')
#fts.write(str(int(num_time_steps))+'\n'+str(num_outputs))
#fts.close()
#exitStatus,stdOutput,stdError = RapptureExec(["python", "run_prismspf_simulation.py"])
if (exitStatus == 0):
simulationCompleted = True
# Group the files
subprocess.call(["mkdir", run_name])
for output_files in glob.glob('*vtu'):
shutil.move(output_files, run_name)
if os.path.exists("integratedFields.txt") is True:
shutil.move("integratedFields.txt", run_name)
# shutil.move(run_name, rappture_path)
else:
simulationCompleted = False
os.chdir(rappture_path)
return simulationCompleted
'''
def call_lammps(simulation, np, nanohub, prefix='mpiexec'):
"""pysimm.lmps.call_lammps
Wrapper to call LAMMPS using executable name defined in pysimm.lmps module.
Args:
simulation: :class:`~pysimm.lmps.Simulation` object reference
np: number of threads to use
nanohub: dictionary containing nanohub resource information default=None
prefix: prefix for running LAMMPS (i.e. - mpiexec)
Returns:
None
"""
log_name = simulation.log or 'log.lammps'
if nanohub:
with open('temp.in', 'w') as f:
f.write(simulation.input)
if simulation.name:
print('%s: sending %s simulation to computer cluster at nanoHUB' %
(strftime('%H:%M:%S'), simulation.name))
else:
print('%s: sending simulation to computer cluster at nanoHUB' %
strftime('%H:%M:%S'))
sys.stdout.flush()
cmd = ('submit -n %s -w %s -i temp.lmps -i temp.in '
'lammps-09Dec14-parallel -e both -l none -i temp.in' %
(nanohub.get('cores'), nanohub.get('walltime')))
cmd = shlex.split(cmd)
exit_status, stdo, stde = RapptureExec(cmd)
else:
if simulation.name:
print('%s: starting %s LAMMPS simulation' %
(strftime('%H:%M:%S'), simulation.name))
else:
print('%s: starting LAMMPS simulation' % strftime('%H:%M:%S'))
if np:
p = Popen([prefix, '-np',
str(np), LAMMPS_EXEC, '-e', 'both'],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
else:
p = Popen([LAMMPS_EXEC, '-e', 'both'],
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
simulation.write_input()
if simulation.debug:
print(simulation.input)
warning_print(
'debug setting involves streaming output from LAMMPS process and can degrade performance'
)
warning_print(
'only use debug for debugging purposes, use print_to_screen to collect stdout after process finishes'
)
p.stdin.write(simulation.input.encode('utf-8'))
q = Queue()
t = Thread(target=enqueue_output, args=(p.stdout, q))
t.daemon = True
t.start()
while t.is_alive() or not q.empty():
try:
line = q.get_nowait()
except Empty:
pass
else:
if simulation.debug:
sys.stdout.write(line.decode('utf-8'))
sys.stdout.flush()
else:
stdo, stde = p.communicate(simulation.input.encode('utf-8'))
if simulation.print_to_screen:
print(stdo.decode('utf-8'))
print(stde.decode('utf-8'))
simulation.system.read_lammps_dump('pysimm.dump.tmp')
try:
os.remove('temp.lmps')
except OSError as e:
print(str(e))
if os.path.isfile('pysimm.qeq.tmp'):
os.remove('pysimm.qeq.tmp')
try:
os.remove('pysimm.dump.tmp')
if simulation.name:
print('%s: %s simulation using LAMMPS successful' %
(strftime('%H:%M:%S'), simulation.name))
else:
print('%s: simulation using LAMMPS successful' %
(strftime('%H:%M:%S')))
except OSError as e:
if simulation.name:
raise PysimmError('%s simulation using LAMMPS UNsuccessful' %
simulation.name)
else:
raise PysimmError('simulation using LAMMPS UNsuccessful')
def minimize(s, template=None, **kwargs):
"""pysimm.lmps.minimize
Convenience function for performing LAMMPS energy minimization
*** WILL BE DEPRECATED - USE QUICK_MIN INSTEAD ***
"""
global LAMMPS_EXEC
if template:
template.update(kwargs)
kwargs = template
name = kwargs.get('name') or False
log = kwargs.get('log') or 'log.lammps'
write = kwargs.get('write') or False
print_to_screen = kwargs.get('print_to_screen') if kwargs.get(
'print_to_screen') is not None else False
special_bonds = kwargs.get('special_bonds') or 'amber'
cutoff = kwargs.get('cutoff') or 12.0
min_style = kwargs.get('min_style')
fire_etol = kwargs.get('sd_etol') or 1.0e-3
fire_ftol = kwargs.get('sd_ftol') or 1.0e-3
fire_maxiter = kwargs.get('sd_maxiter') or 10000
fire_maxeval = kwargs.get('sd_maxeval') or 100000
sd_etol = kwargs.get('sd_etol') or 1.0e-3
sd_ftol = kwargs.get('sd_ftol') or 1.0e-3
sd_maxiter = kwargs.get('sd_maxiter') or 10000
sd_maxeval = kwargs.get('sd_maxeval') or 100000
cg_etol = kwargs.get('cg_etol') or 1.0e-6
cg_ftol = kwargs.get('cg_ftol') or 1.0e-6
cg_maxiter = kwargs.get('cg_maxiter') or 10000
cg_maxeval = kwargs.get('cg_maxeval') or 100000
thermo = kwargs.get('thermo') or 1000
thermo_style = kwargs.get('thermo_style')
nonbond_mixing = kwargs.get('nonbond_mixing')
kspace_style = kwargs.get('kspace_style') or 'pppm 1e-4'
nanohub = kwargs.get('nanohub') or {}
pbs = kwargs.get('pbs')
np = kwargs.get('np')
command = write_init(s, nb_cut=cutoff, special_bonds=special_bonds,
nonbond_mixing=nonbond_mixing, kspace_style=kspace_style)
if log:
command += 'log %s append\n' % log
elif name:
command += 'log %s.log append\n' % '_'.join(name.split())
else:
command += 'log log.lammps append\n'
if thermo:
command += 'thermo %s\n' % int(thermo)
if thermo_style:
command += 'thermo_style %s\n' % thermo_style
if not min_style or min_style == 'sd':
command += 'min_style sd\n'
command += ('minimize %s %s %s %s\n'
% (sd_etol, sd_ftol, sd_maxiter, sd_maxeval))
command += 'min_style cg\n'
command += ('minimize %s %s %s %s\n'
% (cg_etol, cg_ftol, cg_maxiter, cg_maxeval))
elif min_style == 'fire':
command += 'timestep 1\n'
command += 'min_style fire\n'
command += ('minimize %s %s %s %s\n'
% (fire_etol, fire_ftol, fire_maxiter, fire_maxeval))
if write:
command += 'write_data %s\n' % write
else:
command += 'write_data pysimm_min.lmps\n'
with open('temp.in', 'w') as f:
f.write(command)
if name:
print('%s: starting %s simulation using LAMMPS'
% (strftime('%H:%M:%S'), name))
else:
print('%s: starting minimization using LAMMPS'
% strftime('%H:%M:%S'))
if nanohub:
if name:
print('%s: sending %s simulation to computer cluster' % (strftime('%H:%M:%S'), name))
sys.stdout.flush()
cmd = ('submit -n %s -w %s -i temp.lmps -i temp.in '
'lammps-09Dec14-parallel -e both -l none -i temp.in'
% (nanohub.get('cores'), nanohub.get('walltime')))
cmd = shlex.split(cmd)
exit_status, stdo, stde = RapptureExec(cmd)
if pbs:
call('mpiexec %s -e both -l log' % LAMMPS_EXEC, shell=True,
stdin=open('temp.in'), stdout=PIPE, stderr=PIPE)
else:
if np:
p = Popen(['mpiexec', '-np', str(np),
LAMMPS_EXEC, '-e', 'both', '-l', 'none'],
stdin=open('temp.in'), stdout=PIPE, stderr=PIPE)
else:
p = Popen([LAMMPS_EXEC, '-e', 'both', '-l', 'none'],
stdin=open('temp.in'), stdout=PIPE, stderr=PIPE)
while True:
out = p.stdout.read(1)
if out == '' and p.poll() is not None:
break
if out != '' and print_to_screen:
sys.stdout.write(out)
sys.stdout.flush()
if write:
n = read_lammps(write, quiet=True,
pair_style=s.pair_style,
bond_style=s.bond_style,
angle_style=s.angle_style,
dihedral_style=s.dihedral_style,
improper_style=s.improper_style)
else:
n = read_lammps('pysimm_min.lmps', quiet=True,
pair_style=s.pair_style,
bond_style=s.bond_style,
angle_style=s.angle_style,
dihedral_style=s.dihedral_style,
improper_style=s.improper_style)
for p in n.particles:
s.particles[p.tag].x = p.x
s.particles[p.tag].y = p.y
s.particles[p.tag].z = p.z
os.remove('temp.in')
try:
os.remove('temp.lmps')
except OSError as e:
print e
if not write:
try:
os.remove('pysimm_min.lmps')
if name:
print('%s: %s simulation using LAMMPS successful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: minimization using LAMMPS successful'
% (strftime('%H:%M:%S')))
return True
except OSError:
if name:
print('%s: %s simulation using LAMMPS UNsuccessful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: minimization using LAMMPS UNsuccessful'
% strftime('%H:%M:%S'))
return False
else:
if os.path.isfile(write):
if name:
print('%s: %s simulation using LAMMPS successful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: minimization using LAMMPS successful'
% (strftime('%H:%M:%S')))
return True
else:
if name:
print('%s: %s simulation using LAMMPS UNsuccessful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: minimization using LAMMPS UNsuccessful'
% strftime('%H:%M:%S'))
return False
def md(s, template=None, **kwargs):
"""pysimm.lmps.md
Convenience function for performing LAMMPS MD
*** WILL BE DEPRECATED - USE QUICK_MD INSTEAD ***
"""
global LAMMPS_EXEC
if template:
template.update(kwargs)
kwargs = template
name = kwargs.get('name') or False
log = kwargs.get('log')
write = kwargs.get('write') or False
print_to_screen = kwargs.get('print_to_screen') if kwargs.get(
'print_to_screen') is not None else False
special_bonds = kwargs.get('special_bonds') or 'amber'
cutoff = kwargs.get('cutoff') or 12.0
timestep = kwargs.get('timestep') or 1
ensemble = kwargs.get('ensemble') or 'nvt'
temp = kwargs.get('temp')
pressure = kwargs.get('pressure') or 1.
new_v = kwargs.get('new_v')
seed = kwargs.get('seed') or randint(10000, 99999)
scale_v = kwargs.get('scale_v')
length = kwargs.get('length') or 2000
thermo = kwargs.get('thermo') or 1000
thermo_style = kwargs.get('thermo_style')
nonbond_mixing = kwargs.get('nonbond_mixing')
kspace_style = kwargs.get('kspace_style') or 'pppm 1e-4'
nanohub = kwargs.get('nanohub') or {}
pbs = kwargs.get('pbs')
np = kwargs.get('np')
kokkos = kwargs.get('kokkos')
dump = kwargs.get('dump') or False
dump_name = kwargs.get('dump_name')
dump_append = kwargs.get('dump_append')
if temp is None:
t_start = kwargs.get('t_start')
t_stop = kwargs.get('t_stop')
if t_start is None:
t_start = 1000.
if t_stop is None:
t_stop = t_start
else:
t_start = temp
t_stop = temp
command = write_init(s, nb_cut=cutoff, special_bonds=special_bonds,
nonbond_mixing=nonbond_mixing, kspace_style=kspace_style)
if log:
command += 'log %s append\n' % log
elif name:
command += 'log %s.log append\n' % '_'.join(name.split())
else:
command += 'log log.lammps append\n'
if thermo:
command += 'thermo %s\n' % int(thermo)
if thermo_style:
command += 'thermo_style %s\n' % thermo_style
command += 'timestep %s\n' % timestep
if ensemble == 'nvt':
command += 'fix 1 all %s temp %s %s 100\n' % (ensemble, t_start, t_stop)
elif ensemble == 'npt':
command += ('fix 1 all %s temp %s %s 100 iso %s %s 100\n'
% (ensemble, t_start, t_stop, pressure, pressure))
if new_v:
command += 'velocity all create %s %s\n' % (t_start, seed)
elif scale_v:
command += 'velocity all scale %s\n' % t_start
if dump:
if dump_name:
command += ('dump pysimm_dump all atom %s %s.lammpstrj\n'
% (dump, dump_name))
elif name:
command += ('dump pysimm_dump all atom %s %s.lammpstrj\n'
% (dump, '_'.join(name.split())))
else:
command += ('dump pysimm_dump all atom %s pysimm_dump.lammpstrj\n'
% dump)
if dump_append:
command += 'dump_modify pysimm_dump append yes\n'
command += 'run %s\n' % length
command += 'unfix 1\n'
if write:
command += 'write_data %s\n' % write
else:
command += 'write_data pysimm_md.lmps\n'
with open('temp.in', 'w') as f:
f.write(command)
if name:
print('%s: starting %s simulation using LAMMPS'
% (strftime('%H:%M:%S'), name))
else:
print('%s: starting molecular dynamics using LAMMPS'
% strftime('%H:%M:%S'))
if nanohub:
if name:
print('%s: sending %s simulation to computer cluster' % (strftime('%H:%M:%S'), name))
sys.stdout.flush()
cmd = ('submit -n %s -w %s -i temp.lmps -i temp.in '
'lammps-09Dec14-parallel -e both -l none -i temp.in'
% (nanohub.get('cores'), nanohub.get('walltime')))
cmd = shlex.split(cmd)
exit_status, stdo, stde = RapptureExec(cmd)
elif pbs:
call('mpiexec %s -e both -l log' % LAMMPS_EXEC, shell=True,
stdin=open('temp.in'), stdout=PIPE, stderr=PIPE)
else:
if np:
p = Popen(['mpiexec', '-np', str(np),
LAMMPS_EXEC, '-e', 'both', '-l', 'none'],
stdin=open('temp.in'), stdout=PIPE, stderr=PIPE)
elif kokkos:
p = Popen([LAMMPS_EXEC, '-k', 'on', '-sf', 'kk', '-e', 'both', '-l', 'none'],
stdin=open('temp.in'), stdout=PIPE, stderr=PIPE)
else:
p = Popen([LAMMPS_EXEC, '-e', 'both', '-l', 'none'],
stdin=open('temp.in'), stdout=PIPE, stderr=PIPE)
while True:
out = p.stdout.read(1)
if out == '' and p.poll() is not None:
break
if out != '' and print_to_screen:
sys.stdout.write(out)
sys.stdout.flush()
if write:
n = read_lammps(write, quiet=True,
pair_style=s.pair_style,
bond_style=s.bond_style,
angle_style=s.angle_style,
dihedral_style=s.dihedral_style,
improper_style=s.improper_style)
else:
n = read_lammps('pysimm_md.lmps', quiet=True,
pair_style=s.pair_style,
bond_style=s.bond_style,
angle_style=s.angle_style,
dihedral_style=s.dihedral_style,
improper_style=s.improper_style)
for p in n.particles:
p_ = s.particles[p.tag]
p_.x = p.x
p_.y = p.y
p_.z = p.z
p_.vx = p.vx
p_.vy = p.vy
p_.vz = p.vz
s.dim = n.dim
os.remove('temp.in')
try:
os.remove('temp.lmps')
except OSError as e:
print e
if not write:
try:
os.remove('pysimm_md.lmps')
if name:
print('%s: %s simulation using LAMMPS successful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: molecular dynamics using LAMMPS successful'
% (strftime('%H:%M:%S')))
return True
except OSError:
if name:
print('%s: %s simulation using LAMMPS UNsuccessful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: molecular dynamics using LAMMPS UNsuccessful'
% strftime('%H:%M:%S'))
return False
else:
if os.path.isfile(write):
if name:
print('%s: %s simulation using LAMMPS successful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: molecular dynamics using LAMMPS successful'
% (strftime('%H:%M:%S')))
return True
else:
if name:
print('%s: %s simulation using LAMMPS UNsuccessful'
% (strftime('%H:%M:%S'), name))
else:
print('%s: molecular dynamics using LAMMPS UNsuccessful'
% strftime('%H:%M:%S'))
return False
def call_lammps(simulation, np, nanohub):
"""pysimm.lmps.call_lammps
Wrapper to call LAMMPS using executable name defined in pysimm.lmps module.
Args:
simulation: pysimm.lmps.Simulation object reference
np: number of threads to use
nanohub: dictionary containing nanohub resource information default=None
Returns:
None
"""
if nanohub:
if simulation.name:
print('%s: sending %s simulation to computer cluster at nanoHUB' % (strftime('%H:%M:%S'), simulation.name))
sys.stdout.flush()
cmd = ('submit -n %s -w %s -i temp.lmps -i temp.in '
'lammps-09Dec14-parallel -e both -l none -i temp.in'
% (nanohub.get('cores'), nanohub.get('walltime')))
cmd = shlex.split(cmd)
exit_status, stdo, stde = RapptureExec(cmd)
else:
if simulation.name:
print('%s: starting %s simulation using LAMMPS'
% (strftime('%H:%M:%S'), simulation.name))
else:
print('%s: starting simulation using LAMMPS'
% strftime('%H:%M:%S'))
if np:
p = Popen(['mpiexec', '-np', str(np),
LAMMPS_EXEC, '-e', 'both', '-l', 'none'],
stdin=PIPE, stdout=PIPE, stderr=PIPE)
else:
p = Popen(['mpiexec', LAMMPS_EXEC, '-e', 'both', '-l', 'none'],
stdin=PIPE, stdout=PIPE, stderr=PIPE)
simulation.write_input()
p.stdin.write(simulation.input)
q = Queue()
t = Thread(target=enqueue_output, args=(p.stdout, q))
t.daemon = True
t.start()
while t.isAlive() or not q.empty():
try:
line = q.get_nowait()
except Empty:
pass
else:
if simulation.print_to_screen:
sys.stdout.write(line)
sys.stdout.flush()
simulation.system.read_lammps_dump('pysimm.dump.tmp')
'''if simulation.write:
n = read_lammps(simulation.write, quiet=True,
pair_style=simulation.system.pair_style,
bond_style=simulation.system.bond_style,
angle_style=simulation.system.angle_style,
dihedral_style=simulation.system.dihedral_style,
improper_style=simulation.system.improper_style)
else:
n = read_lammps('pysimm_md.lmps', quiet=True,
pair_style=simulation.system.pair_style,
bond_style=simulation.system.bond_style,
angle_style=simulation.system.angle_style,
dihedral_style=simulation.system.dihedral_style,
improper_style=simulation.system.improper_style)
for p in n.particles:
p_ = simulation.system.particles[p.tag]
p_.x = p.x
p_.y = p.y
p_.z = p.z
p_.vx = p.vx
p_.vy = p.vy
p_.vz = p.vz
simulation.system.dim = n.dim'''
try:
os.remove('temp.lmps')
except OSError as e:
print e
if os.path.isfile('pysimm.qeq.tmp'):
os.remove('pysimm.qeq.tmp')
try:
os.remove('pysimm.dump.tmp')
if simulation.name:
print('%s: %s simulation using LAMMPS successful'
% (strftime('%H:%M:%S'), simulation.name))
else:
print('%s: molecular dynamics using LAMMPS successful'
% (strftime('%H:%M:%S')))
except OSError as e:
if simulation.name:
raise PysimmError('%s simulation using LAMMPS UNsuccessful' % simulation.name)
else:
raise PysimmError('molecular dynamics using LAMMPS UNsuccessful')
'''if not simulation.write:
def network(s, **kwargs):
"""pysimm.apps.zeopp.network
Perform 1. Pore diameters; 2. Channel identification and dimensionality; 3. Surface area;
4. Accessible volume; 5. Pore size distribution calculation using zeo++ v2.2
with options to do 6. Probe-occupiable volume; 7. Stochastic ray tracing; 8. Blocking spheres;
9. Distance grids; 10. Structure analysis
Args:
s: pysimm System object or filename of file in CSSR | CUC | V1 | CIF format
atype_name: True to use atom type as atom name (usually need radii and mass info), False to use atom element
radii: file name that contain atom radii data (rad.rad)
mass: file name that contain atom mass data (mass.mass)
probe_radius: radius of a probe used in sampling of surface (1.2 A)
chan_radius: radius of a probe used to determine accessibility of void space (1.2 A)
num_samples: number of Monte Carlo samples per unit cell (50000)
option to include in the simulation: set True to activate
ha: default=True, for using high accuracy,
res: default=True, for diameters of the largest included sphere, the largest free sphere and the largest included sphere along free sphere path
chan: default=True, for channel systems characterized by dimensionality as well as Di, Df and Dif
sa: default=True, for surface area accessible to a spherical probe, characterized by
accessible surface area (ASA) and non-accessible surface area (NASA)
vol: default=True, for accessible volume (AV) and non-accessible volume (NAV)
volpo: default=False, for accessible proce-occupiable volume (POAV) and non-accessible probe-occupiable volume (PONAV)
psd: default=True, for the "deriviative distribution" (change of AV w.r.t probe size) reported in the histogram file with 1000 bins of size of 0.1 Ang
ray_atom: default=False
block: default=False
extra: user provided options, such as -gridG, -gridBOV, -strinfo, -oms, etc.
ZEOpp_EXEC: path to zeo++ executable (network)
Returns:
None
"""
global ZEOpp_EXEC
if ZEOpp_EXEC is None:
print('Please specify the environment variable '
'ZEOpp_EXEC'
' that points to '
'zeo++ executable (network)')
exit(1)
probe_radius = kwargs.get('probe_radius', 1.2)
chan_radius = kwargs.get('chan_radius', 1.2)
num_samples = kwargs.get('num_samples', 50000)
atype_name = kwargs.get('atype_name', False)
ha = kwargs.get('ha', True)
res = kwargs.get('res', True)
chan = kwargs.get('chan', True)
sa = kwargs.get('sa', True)
vol = kwargs.get('vol', True)
psd = kwargs.get('psd', True)
volpo = kwargs.get('volpo', False)
ray_atom = kwargs.get('ray_atom', False)
block = kwargs.get('block', False)
extra = kwargs.get('extra')
nanohub = kwargs.get('nanohub')
if isinstance(s, system.System):
if atype_name:
s.write_cssr('zeopp_data.cssr', aname=1)
else:
s.write_cssr('zeopp_data.cssr')
input_file = 'zeopp_data.cssr'
elif isinstance(s, str):
input_file = s
args = ZEOpp_EXEC
if 'radii' in kwargs.keys():
args += ' -r ' + kwargs.get('radii')
if 'mass' in kwargs.keys():
args += ' -mass ' + kwargs.get('mass')
if ha:
args += ' -ha'
if res:
args += ' -res'
if chan:
args += ' -chan ' + str(probe_radius)
if sa:
args += ' -sa ' + str(chan_radius) + ' ' + str(
probe_radius) + ' ' + str(num_samples)
if vol:
args += ' -vol ' + str(chan_radius) + ' ' + str(
probe_radius) + ' ' + str(num_samples)
if psd:
args += ' -psd ' + str(chan_radius) + ' ' + str(
probe_radius) + ' ' + str(num_samples)
if volpo:
args += ' -volpo ' + str(chan_radius) + ' ' + str(
probe_radius) + ' ' + str(num_samples)
if ray_atom:
args += ' -ray_atom ' + str(chan_radius) + ' ' + str(
probe_radius) + ' ' + str(num_samples)
if block:
args += ' -block ' + str(probe_radius) + ' ' + str(num_samples)
if extra:
args += ' ' + extra
args += ' ' + input_file
arg_list = shlex.split(args)
print('%s: starting simulation using zeo++' % strftime('%H:%M:%S'))
if nanohub:
print('%s: sending zeo++ simulation to computer cluster' %
strftime('%H:%M:%S'))
sys.stdout.flush()
cmd = ('submit -n 1 -w %s ' % (24 * 60)) + ZEOpp_EXEC + args
cmd = shlex.split(cmd)
exit_status, stdo, stde = RapptureExec(cmd)
else:
p = Popen(arg_list, stdin=PIPE, stdout=PIPE, stderr=PIPE)
while True:
stout = p.stdout.readline()
if stout == '' and p.poll() is not None:
break
if stout:
print(stout.strip())
# print(stout)
sterr = p.stderr.readlines()
print(sterr)
print('%s: zeo++ simulation successful' % strftime('%H:%M:%S'))