def main(argv=sys.argv, log_output=True, return_output_fname=False,
return_results_dict=False, field=None, lspr_values=None):
"""
Run a PyGBe problem, write outputs to STDOUT and to log file in
problem directory
Arguments
----------
log_output : Bool, default True.
If False, output is written only to STDOUT and not to a log file.
return_output_fname: Bool, default False.
If True, function main() returns the name of the
output log file. This is used for the regression tests.
return_results_dict: Bool, default False.
If True, function main() returns the results of the run
packed in a dictionary. Used in testing and programmatic
use of PyGBe
field : Dictionary, defaults to None.
If passed, this dictionary will supercede any config file found, useful in
programmatically stepping through slight changes in a problem.
lspr_values : list, defaults to None
If passed, provides values for `electric_field` and `wavelength`, useful to
programmatically step through varying wavelengths
Returns
--------
output_fname : str, if kwarg is True.
The name of the log file containing problem output
"""
args = read_inputs(argv[1:])
configFile, paramfile = find_config_files(args)
full_path = os.environ.get('PYGBE_PROBLEM_FOLDER')
#check if a custom geometry location has been specified
#if it has, add an ENV_VAR to handle it
if args.geometry:
geo_path = os.path.abspath(args.geometry)
if os.path.isdir(geo_path):
os.environ['PYGBE_GEOMETRY'] = geo_path
else:
sys.exit('Invalid geometry prefix provided (Folder not found)')
else:
geo_path = os.path.join(full_path, 'geometry')
#try to expand ~ if present in output path
args.output = os.path.expanduser(args.output)
#if output path is absolute, use that, otherwise prepend
#problem path
if not os.path.isdir(args.output):
output_dir = os.path.join(full_path, args.output)
else:
output_dir = args.output
# create output directory if it doesn't already exist
try:
os.makedirs(output_dir)
except OSError:
pass
results_dict = {}
timestamp = time.localtime()
outputfname = '{:%Y-%m-%d-%H%M%S}-output.log'.format(datetime.now())
results_dict['output_file'] = outputfname
if log_output:
restore_stdout = sys.stdout
sys.stdout = Logger(os.path.join(output_dir, outputfname))
# Time stamp
print('Run started on:')
print('\tDate: {}/{}/{}'.format(timestamp.tm_year, timestamp.tm_mon,
timestamp.tm_mday))
print('\tTime: {}:{}:{}'.format(timestamp.tm_hour, timestamp.tm_min,
timestamp.tm_sec))
print('\tPyGBe version: {}'.format(pygbe.__version__))
TIC = time.time()
print('Config file: {}'.format(configFile))
print('Parameter file: {}'.format(paramfile))
print('Geometry folder: {}'.format(geo_path))
print('Running in: {}'.format(full_path))
results_dict['config_file'] = configFile
results_dict['param_file'] = paramfile
results_dict['geo_file'] = geo_path
results_dict['full_path'] = full_path
### Read parameters
param = Parameters()
precision = read_parameters(param, paramfile)
param.Nm = (param.P + 1) * (param.P + 2) * (
param.P + 3) // 6 # Number of terms in Taylor expansion
param.BlocksPerTwig = int(numpy.ceil(param.NCRIT / float(param.BSZ))
) # CUDA blocks that fit per twig
HAS_GPU = check_for_nvcc()
if param.GPU == 1 and not HAS_GPU:
print('\n\n\n\n')
print('{:-^{}}'.format('No GPU DETECTED', 60))
print("Your param file has `GPU = 1` but CUDA was not detected.\n"
"Continuing using CPU. If you do not want this, use Ctrl-C\n"
"to stop the program and check that your CUDA installation\n"
"is on your $PATH")
print('{:-^{}}'.format('No GPU DETECTED', 60))
print('\n\n\n\n')
param.GPU = 0
### Generate array of fields
if field:
field_array = initialize_field(configFile, param, field)
else:
field_array = initialize_field(configFile, param)
### Generate array of surfaces and read in elements
surf_array = initialize_surface(field_array, configFile, param)
### Read electric field and its wavelength.
if lspr_values:
electric_field, wavelength = lspr_values
else:
electric_field, wavelength = read_electric_field(param, configFile)
### Fill surface class
time_sort = 0.
for i in range(len(surf_array)):
time_sort += surf_array[i].fill_surface(param)
### Output setup summary
param.N = 0
param.Neq = 0
for s in surf_array:
N_aux = len(s.triangle)
param.N += N_aux
if s.surf_type in ['dirichlet_surface', 'neumann_surface', 'asc_surface']:
param.Neq += N_aux
else:
param.Neq += 2 * N_aux
print('\nTotal elements : {}'.format(param.N))
print('Total equations: {}'.format(param.Neq))
results_dict['total_elements'] = param.N
results_dict['N_equation'] = param.Neq
results_dict = print_summary(surf_array, field_array, param, results_dict)
### Precomputation
ind0 = IndexConstant()
computeIndices(param.P, ind0)
precomputeTerms(param.P, ind0)
### Load CUDA code
if param.GPU == 1:
kernel = kernels(param.BSZ, param.Nm, param.K_fine, param.P, precision)
else:
kernel = 1
### Generate interaction list
print('Generate interaction list')
tic = time.time()
generateList(surf_array, field_array, param)
toc = time.time()
list_time = toc - tic
### Transfer data to GPU
print('Transfer data to GPU')
tic = time.time()
if param.GPU == 1:
dataTransfer(surf_array, field_array, ind0, param, kernel)
toc = time.time()
transfer_time = toc - tic
timing = Timing()
### Generate RHS
print('Generate RHS')
tic = time.time()
if param.GPU == 0:
F = generateRHS(field_array, surf_array, param, kernel, timing, ind0, electric_field)
elif param.GPU == 1:
F = generateRHS_gpu(field_array, surf_array, param, kernel, timing,
ind0, electric_field)
toc = time.time()
rhs_time = toc - tic
setup_time = toc - TIC
print('List time : {}s'.format(list_time))
print('Data transfer time : {}s'.format(transfer_time))
print('RHS generation time: {}s'.format(rhs_time))
print('-'*30)
print('Total setup time : {}s'.format(setup_time))
# Check if there is a complex dielectric
if any([numpy.iscomplexobj(f.E) for f in field_array]):
complex_diel = True
else:
complex_diel = False
### Solve
tic = time.time()
print('Solve')
# Initializing phi dtype according to the problem we are solving.
if complex_diel:
phi = numpy.zeros(param.Neq, dtype=numpy.complex)
else:
raise ValueError('Dielectric should be complex for LSPR problems')
phi, iteration = gmres_mgs(surf_array, field_array, phi, F, param, ind0,
timing, kernel)
toc = time.time()
results_dict['iterations'] = iteration
solve_time = toc - tic
print('Solve time : {}s'.format(solve_time))
phifname = '{:%Y-%m-%d-%H%M%S}-phi_{}.txt'.format(datetime.now(), wavelength)
results_dict['solve_time'] = solve_time
numpy.savetxt(os.path.join(output_dir, phifname), phi)
# Put result phi in corresponding surfaces
s_start = 0
for surf in surf_array:
s_start = surf.fill_phi(phi, s_start)
#Calculate extinction cross section for lspr problems
if abs(electric_field) > 1e-12:
###Calculating the dipole moment
dipole_moment(surf_array, electric_field)
print('\nCalculate extinction cross section (Cext)')
tic = time.time()
Cext, surf_Cext = extinction_cross_section(surf_array, numpy.array([1,0,0]), numpy.array([0,0,1]),
wavelength, electric_field)
toc = time.time()
print('Time Cext: {}s'.format(toc - tic))
print('\nWavelength: {:.2f} nm'.format(wavelength/10))
print('Incoming Electric Field: {:.4f} e/(Ang^2 eps_0)'.format(electric_field))
print('\nCext per surface')
for i in range(len(Cext)):
print('Surface {}: {} nm^2'.format(surf_Cext[i], Cext[i]))
results_dict['time_Cext'] = toc - tic
results_dict['surf_Cext'] = surf_Cext
results_dict['wavelength'] = wavelength
results_dict['E_field'] = electric_field
results_dict['Cext_list'] = Cext
results_dict['Cext_0'] = Cext[0] #We do convergence analysis in the main sphere
else:
raise ValueError('electric_field should not be zero to calculate'
'the extinction cross section')
results_dict['total_time'] = (toc - TIC)
results_dict['version'] = pygbe.__version__
output_pickle = outputfname.split('-')
output_pickle.pop(-1)
output_pickle.append('resultspickle_'+str(wavelength))
output_pickle = '-'.join(output_pickle)
with open(os.path.join(output_dir, output_pickle), 'wb') as f:
pickle.dump(results_dict, f, 2)
try:
with open(os.path.join(output_dir, output_pickle), 'rb') as f:
pickle.load(f)
except EOFError:
print('Error writing the pickle file, the results will be unreadable')
pass
#reset stdout so regression tests, etc, don't get logged into the output
#file that they themselves are trying to read
if log_output:
sys.stdout = restore_stdout
if return_results_dict:
return results_dict
if return_output_fname and log_output:
return outputfname
def main(argv=sys.argv,
log_output=True,
return_output_fname=False,
return_results_dict=False,
field=None):
"""
Run a PyGBe problem, write outputs to STDOUT and to log file in
problem directory
Arguments
----------
log_output : Bool, default True.
If False, output is written only to STDOUT and not to a log file.
return_output_fname: Bool, default False.
If True, function main() returns the name of the
output log file. This is used for the regression tests.
return_results_dict: Bool, default False.
If True, function main() returns the results of the run
packed in a dictionary. Used in testing and programmatic
use of PyGBe
field : Dictionary, defaults to None.
If passed, this dictionary will supercede any config file found, useful in
programmatically stepping through slight changes in a problem
Returns
--------
output_fname : str, if kwarg is True.
The name of the log file containing problem output
"""
args = read_inputs(argv[1:])
configFile, paramfile = find_config_files(args)
full_path = os.environ.get('PYGBE_PROBLEM_FOLDER')
#check if a custom geometry location has been specified
#if it has, add an ENV_VAR to handle it
if args.geometry:
geo_path = os.path.abspath(args.geometry)
if os.path.isdir(geo_path):
os.environ['PYGBE_GEOMETRY'] = geo_path
else:
sys.exit('Invalid geometry prefix provided (Folder not found)')
else:
geo_path = os.path.join(full_path, 'geometry')
#try to expand ~ if present in output path
args.output = os.path.expanduser(args.output)
#if output path is absolute, use that, otherwise prepend
#problem path
if not os.path.isdir(args.output):
output_dir = os.path.join(full_path, args.output)
else:
output_dir = args.output
# create output directory if it doesn't already exist
try:
os.makedirs(output_dir)
except OSError:
pass
results_dict = {}
timestamp = time.localtime()
outputfname = '{:%Y-%m-%d-%H%M%S}-output.log'.format(datetime.now())
results_dict['output_file'] = outputfname
if log_output:
restore_stdout = sys.stdout
sys.stdout = Logger(os.path.join(output_dir, outputfname))
# Time stamp
print('Run started on:')
print('\tDate: {}/{}/{}'.format(timestamp.tm_year, timestamp.tm_mon,
timestamp.tm_mday))
print('\tTime: {}:{}:{}'.format(timestamp.tm_hour, timestamp.tm_min,
timestamp.tm_sec))
print('\tPyGBe version: {}'.format(pygbe.__version__))
TIC = time.time()
print('Config file: {}'.format(configFile))
print('Parameter file: {}'.format(paramfile))
print('Geometry folder: {}'.format(geo_path))
print('Running in: {}'.format(full_path))
results_dict['config_file'] = configFile
results_dict['param_file'] = paramfile
results_dict['geo_file'] = geo_path
results_dict['full_path'] = full_path
### Read parameters
param = Parameters()
precision = read_parameters(param, paramfile)
param.Nm = (param.P + 1) * (param.P + 2) * (
param.P + 3) // 6 # Number of terms in Taylor expansion
param.BlocksPerTwig = int(numpy.ceil(
param.NCRIT / float(param.BSZ))) # CUDA blocks that fit per twig
HAS_GPU = check_for_nvcc()
if param.GPU == 1 and not HAS_GPU:
print('\n\n\n\n')
print('{:-^{}}'.format('No GPU DETECTED', 60))
print("Your param file has `GPU = 1` but CUDA was not detected.\n"
"Continuing using CPU. If you do not want this, use Ctrl-C\n"
"to stop the program and check that your CUDA installation\n"
"is on your $PATH")
print('{:-^{}}'.format('No GPU DETECTED', 60))
print('\n\n\n\n')
param.GPU = 0
### Generate array of fields
if field:
field_array = initialize_field(configFile, param, field)
else:
field_array = initialize_field(configFile, param)
### Generate array of surfaces and read in elements
surf_array = initialize_surface(field_array, configFile, param)
### Fill surface class
time_sort = 0.
for i in range(len(surf_array)):
time_sort += surf_array[i].fill_surface(param)
### Output setup summary
param.N = 0
param.Neq = 0
for s in surf_array:
N_aux = len(s.triangle)
param.N += N_aux
if s.surf_type in [
'dirichlet_surface', 'neumann_surface', 'asc_surface'
]:
param.Neq += N_aux
else:
param.Neq += 2 * N_aux
print('\nTotal elements : {}'.format(param.N))
print('Total equations: {}'.format(param.Neq))
results_dict['total_elements'] = param.N
results_dict['N_equation'] = param.Neq
results_dict = print_summary(surf_array, field_array, param, results_dict)
### Precomputation
ind0 = IndexConstant()
computeIndices(param.P, ind0)
precomputeTerms(param.P, ind0)
### Load CUDA code
if param.GPU == 1:
kernel = kernels(param.BSZ, param.Nm, param.K_fine, param.P, precision)
else:
kernel = 1
### Generate interaction list
print('Generate interaction list')
tic = time.time()
generateList(surf_array, field_array, param)
toc = time.time()
list_time = toc - tic
### Transfer data to GPU
print('Transfer data to GPU')
tic = time.time()
if param.GPU == 1:
dataTransfer(surf_array, field_array, ind0, param, kernel)
toc = time.time()
transfer_time = toc - tic
timing = Timing()
### Generate RHS
print('Generate RHS')
tic = time.time()
if param.GPU == 0:
F = generateRHS(field_array, surf_array, param, kernel, timing, ind0)
elif param.GPU == 1:
F = generateRHS_gpu(field_array, surf_array, param, kernel, timing,
ind0)
toc = time.time()
rhs_time = toc - tic
setup_time = toc - TIC
print('List time : {}s'.format(list_time))
print('Data transfer time : {}s'.format(transfer_time))
print('RHS generation time: {}s'.format(rhs_time))
print('-' * 30)
print('Total setup time : {}s'.format(setup_time))
# Check if there is a complex dielectric
if any([numpy.iscomplexobj(f.E) for f in field_array]):
complex_diel = True
else:
complex_diel = False
### Solve
tic = time.time()
print('Solve')
# Initializing phi dtype according to the problem we are solving.
if not complex_diel:
phi = numpy.zeros(param.Neq)
else:
raise ValueError(
'Dielectric should be real for solvation energy problems')
phi, iteration = gmres_mgs(surf_array, field_array, phi, F, param, ind0,
timing, kernel)
toc = time.time()
results_dict['iterations'] = iteration
solve_time = toc - tic
print('Solve time : {}s'.format(solve_time))
phifname = '{:%Y-%m-%d-%H%M%S}-phi.txt'.format(datetime.now())
results_dict['solve_time'] = solve_time
numpy.savetxt(os.path.join(output_dir, phifname), phi)
# Put result phi in corresponding surfaces
s_start = 0
for surf in surf_array:
s_start = surf.fill_phi(phi, s_start)
# Calculate solvation energy
print('Calculate Esolv')
tic = time.time()
E_solv = calculate_solvation_energy(surf_array, field_array, param, kernel)
toc = time.time()
print('Time Esolv: {}s'.format(toc - tic))
ii = -1
for i, f in enumerate(field_array):
if f.pot == 1:
parent_type = surf_array[f.parent[0]].surf_type
if parent_type != 'dirichlet_surface' and parent_type != 'neumann_surface':
ii += 1
print('Region {}: Esolv = {} kcal/mol = {} kJ/mol'.format(
i, E_solv[ii], E_solv[ii] * 4.184))
# Calculate surface energy
print('\nCalculate Esurf')
tic = time.time()
E_surf = calculate_surface_energy(surf_array, field_array, param, kernel)
toc = time.time()
ii = -1
for f in param.E_field:
parent_type = surf_array[field_array[f].parent[0]].surf_type
if parent_type == 'dirichlet_surface' or parent_type == 'neumann_surface':
ii += 1
print('Region {}: Esurf = {} kcal/mol = {} kJ/mol'.format(
f, E_surf[ii], E_surf[ii] * 4.184))
print('Time Esurf: {}s'.format(toc - tic))
### Calculate Coulombic interaction
print('\nCalculate Ecoul')
tic = time.time()
i = -1
E_coul = []
for f in field_array:
i += 1
if f.coulomb == 1:
print('Calculate Coulomb energy for region {}'.format(i))
E_coul.append(coulomb_energy(f, param))
print('Region {}: Ecoul = {} kcal/mol = {} kJ/mol'.format(
i, E_coul[-1], E_coul[-1] * 4.184))
toc = time.time()
print('Time Ecoul: {}s'.format(toc - tic))
### Output summary
print('\n' + '-' * 30)
print('Totals:')
print('Esolv = {} kcal/mol'.format(sum(E_solv)))
print('Esurf = {} kcal/mol'.format(sum(E_surf)))
print('Ecoul = {} kcal/mol'.format(sum(E_coul)))
print('\nTime = {} s'.format(toc - TIC))
results_dict['E_solv_kcal'] = sum(E_solv)
results_dict['E_solv_kJ'] = sum(E_solv) * 4.184
results_dict['E_surf_kcal'] = sum(E_surf)
results_dict['E_surf_kJ'] = sum(E_surf) * 4.184
results_dict['E_coul_kcal'] = sum(E_coul)
results_dict['E_coul_kJ'] = sum(E_coul) * 4.184
results_dict['total_time'] = (toc - TIC)
results_dict['version'] = pygbe.__version__
output_pickle = outputfname.split('-')
output_pickle.pop(-1)
output_pickle.append('resultspickle')
output_pickle = '-'.join(output_pickle)
with open(os.path.join(output_dir, output_pickle), 'wb') as f:
pickle.dump(results_dict, f, 2)
try:
with open(os.path.join(output_dir, output_pickle), 'rb') as f:
pickle.load(f)
except EOFError:
print('Error writing the pickle file, the results will be unreadable')
pass
#reset stdout so regression tests, etc, don't get logged into the output
#file that they themselves are trying to read
if log_output:
sys.stdout = restore_stdout
if return_results_dict:
return results_dict
if return_output_fname and log_output:
return outputfname
def main(argv=sys.argv, log_output=True, return_output_fname=False,
return_results_dict=False, field=None):
"""
Run a PyGBe problem, write outputs to STDOUT and to log file in
problem directory
Arguments
----------
log_output : Bool, default True.
If False, output is written only to STDOUT and not to a log file.
return_output_fname: Bool, default False.
If True, function main() returns the name of the
output log file. This is used for the regression tests.
return_results_dict: Bool, default False.
If True, function main() returns the results of the run
packed in a dictionary. Used in testing and programmatic
use of PyGBe
field : Dictionary, defaults to None.
If passed, this dictionary will supercede any config file found, useful in
programmatically stepping through slight changes in a problem
Returns
--------
output_fname : str, if kwarg is True.
The name of the log file containing problem output
"""
args = read_inputs(argv[1:])
configFile, paramfile = find_config_files(args)
full_path = os.environ.get('PYGBE_PROBLEM_FOLDER')
#check if a custom geometry location has been specified
#if it has, add an ENV_VAR to handle it
if args.geometry:
geo_path = os.path.abspath(args.geometry)
if os.path.isdir(geo_path):
os.environ['PYGBE_GEOMETRY'] = geo_path
else:
sys.exit('Invalid geometry prefix provided (Folder not found)')
else:
geo_path = os.path.join(full_path, 'geometry')
#try to expand ~ if present in output path
args.output = os.path.expanduser(args.output)
#if output path is absolute, use that, otherwise prepend
#problem path
if not os.path.isdir(args.output):
output_dir = os.path.join(full_path, args.output)
else:
output_dir = args.output
# create output directory if it doesn't already exist
try:
os.makedirs(output_dir)
except OSError:
pass
results_dict = {}
timestamp = time.localtime()
outputfname = '{:%Y-%m-%d-%H%M%S}-output.log'.format(datetime.now())
results_dict['output_file'] = outputfname
if log_output:
restore_stdout = sys.stdout
sys.stdout = Logger(os.path.join(output_dir, outputfname))
# Time stamp
print('Run started on:')
print('\tDate: {}/{}/{}'.format(timestamp.tm_year, timestamp.tm_mon,
timestamp.tm_mday))
print('\tTime: {}:{}:{}'.format(timestamp.tm_hour, timestamp.tm_min,
timestamp.tm_sec))
print('\tPyGBe version: {}'.format(pygbe.__version__))
TIC = time.time()
print('Config file: {}'.format(configFile))
print('Parameter file: {}'.format(paramfile))
print('Geometry folder: {}'.format(geo_path))
print('Running in: {}'.format(full_path))
results_dict['config_file'] = configFile
results_dict['param_file'] = paramfile
results_dict['geo_file'] = geo_path
results_dict['full_path'] = full_path
### Read parameters
param = Parameters()
precision = read_parameters(param, paramfile)
param.Nm = (param.P + 1) * (param.P + 2) * (
param.P + 3) // 6 # Number of terms in Taylor expansion
param.BlocksPerTwig = int(numpy.ceil(param.NCRIT / float(param.BSZ))
) # CUDA blocks that fit per twig
HAS_GPU = check_for_nvcc()
if param.GPU == 1 and not HAS_GPU:
print('\n\n\n\n')
print('{:-^{}}'.format('No GPU DETECTED', 60))
print("Your param file has `GPU = 1` but CUDA was not detected.\n"
"Continuing using CPU. If you do not want this, use Ctrl-C\n"
"to stop the program and check that your CUDA installation\n"
"is on your $PATH")
print('{:-^{}}'.format('No GPU DETECTED', 60))
print('\n\n\n\n')
param.GPU = 0
### Generate array of fields
if field:
field_array = initialize_field(configFile, param, field)
else:
field_array = initialize_field(configFile, param)
### Generate array of surfaces and read in elements
surf_array = initialize_surface(field_array, configFile, param)
### Fill surface class
time_sort = 0.
for i in range(len(surf_array)):
time_sort += surf_array[i].fill_surface(param)
### Output setup summary
param.N = 0
param.Neq = 0
for s in surf_array:
N_aux = len(s.triangle)
param.N += N_aux
if s.surf_type in ['dirichlet_surface', 'neumann_surface', 'asc_surface']:
param.Neq += N_aux
else:
param.Neq += 2 * N_aux
print('\nTotal elements : {}'.format(param.N))
print('Total equations: {}'.format(param.Neq))
results_dict['total_elements'] = param.N
results_dict['N_equation'] = param.Neq
results_dict = print_summary(surf_array, field_array, param, results_dict)
### Precomputation
ind0 = IndexConstant()
computeIndices(param.P, ind0)
precomputeTerms(param.P, ind0)
### Load CUDA code
if param.GPU == 1:
kernel = kernels(param.BSZ, param.Nm, param.K_fine, param.P, precision)
else:
kernel = 1
### Generate interaction list
print('Generate interaction list')
tic = time.time()
generateList(surf_array, field_array, param)
toc = time.time()
list_time = toc - tic
### Transfer data to GPU
print('Transfer data to GPU')
tic = time.time()
if param.GPU == 1:
dataTransfer(surf_array, field_array, ind0, param, kernel)
toc = time.time()
transfer_time = toc - tic
timing = Timing()
### Generate RHS
print('Generate RHS')
tic = time.time()
if param.GPU == 0:
F = generateRHS(field_array, surf_array, param, kernel, timing, ind0)
elif param.GPU == 1:
F = generateRHS_gpu(field_array, surf_array, param, kernel, timing,
ind0)
toc = time.time()
rhs_time = toc - tic
setup_time = toc - TIC
print('List time : {}s'.format(list_time))
print('Data transfer time : {}s'.format(transfer_time))
print('RHS generation time: {}s'.format(rhs_time))
print('-'*30)
print('Total setup time : {}s'.format(setup_time))
# Check if there is a complex dielectric
if any([numpy.iscomplexobj(f.E) for f in field_array]):
complex_diel = True
else:
complex_diel = False
### Solve
tic = time.time()
print('Solve')
# Initializing phi dtype according to the problem we are solving.
if not complex_diel:
phi = numpy.zeros(param.Neq)
else:
raise ValueError('Dielectric should be real for solvation energy problems')
phi, iteration = gmres_mgs(surf_array, field_array, phi, F, param, ind0,
timing, kernel)
toc = time.time()
results_dict['iterations'] = iteration
solve_time = toc - tic
print('Solve time : {}s'.format(solve_time))
phifname = '{:%Y-%m-%d-%H%M%S}-phi.txt'.format(datetime.now())
results_dict['solve_time'] = solve_time
numpy.savetxt(os.path.join(output_dir, phifname), phi)
# Put result phi in corresponding surfaces
s_start = 0
for surf in surf_array:
s_start = surf.fill_phi(phi, s_start)
# Calculate solvation energy
print('\nCalculate Solvation Energy (E_solv)')
tic = time.time()
E_solv = calculate_solvation_energy(surf_array, field_array, param, kernel)
toc = time.time()
print('Time E_solv: {}s'.format(toc - tic))
ii = -1
for i, f in enumerate(field_array):
if f.pot == 1:
parent_type = surf_array[f.parent[0]].surf_type
if parent_type != 'dirichlet_surface' and parent_type != 'neumann_surface':
ii += 1
print('Region {}: E_solv = {} kcal/mol = {} kJ/mol'.format(i,
E_solv[ii],
E_solv[ii] * 4.184))
# Calculate surface energy
print('\nCalculate Surface Energy (E_surf)')
tic = time.time()
E_surf = calculate_surface_energy(surf_array, field_array, param, kernel)
toc = time.time()
ii = -1
for f in param.E_field:
parent_type = surf_array[field_array[f].parent[0]].surf_type
if parent_type == 'dirichlet_surface' or parent_type == 'neumann_surface':
ii += 1
print('Region {}: E_surf = {} kcal/mol = {} kJ/mol'.format(
f, E_surf[ii], E_surf[ii] * 4.184))
print('Time E_surf: {}s'.format(toc - tic))
### Calculate Coulombic interaction
print('\nCalculate Coulomb Energy (E_coul)')
tic = time.time()
i = -1
E_coul = []
for f in field_array:
i += 1
if f.coulomb == 1:
print('Calculate Coulomb energy for region {}'.format(i))
E_coul.append(coulomb_energy(f, param))
print('Region {}: E_coul = {} kcal/mol = {} kJ/mol'.format(
i, E_coul[-1], E_coul[-1] * 4.184))
toc = time.time()
print('Time E_coul: {}s'.format(toc - tic))
### Output summary
print('\n'+'-'*30)
print('Totals:')
print('E_solv = {} kcal/mol'.format(sum(E_solv)))
print('E_surf = {} kcal/mol'.format(sum(E_surf)))
print('E_coul = {} kcal/mol'.format(sum(E_coul)))
print('\nTime = {} s'.format(toc - TIC))
results_dict['E_solv_kcal'] = sum(E_solv)
results_dict['E_solv_kJ'] = sum(E_solv) * 4.184
results_dict['E_surf_kcal'] = sum(E_surf)
results_dict['E_surf_kJ'] = sum(E_surf) * 4.184
results_dict['E_coul_kcal'] = sum(E_coul)
results_dict['E_coul_kJ'] = sum(E_coul) * 4.184
results_dict['total_time'] = (toc - TIC)
results_dict['version'] = pygbe.__version__
output_pickle = outputfname.split('-')
output_pickle.pop(-1)
output_pickle.append('resultspickle')
output_pickle = '-'.join(output_pickle)
with open(os.path.join(output_dir, output_pickle), 'wb') as f:
pickle.dump(results_dict, f, 2)
try:
with open(os.path.join(output_dir, output_pickle), 'rb') as f:
pickle.load(f)
except EOFError:
print('Error writing the pickle file, the results will be unreadable')
pass
#reset stdout so regression tests, etc, don't get logged into the output
#file that they themselves are trying to read
if log_output:
sys.stdout = restore_stdout
if return_results_dict:
return results_dict
if return_output_fname and log_output:
return outputfname
def main(argv=sys.argv, log_output=True, return_output_fname=False):
"""
Run a PyGBe problem, write outputs to STDOUT and to log file in
problem directory
Arguments
----------
log_output : Bool, default True.
If False, output is written only to STDOUT and not
to a log file.
return_output_fname: Bool, default False.
If True, function main() returns the name of the
output log file. This is used for the regression tests.
Returns
--------
output_fname : str, if kwarg is True.
The name of the log file containing problem output
"""
args = read_inputs(argv[1:])
configFile, paramfile = find_config_files(args)
full_path = os.environ.get('PYGBE_PROBLEM_FOLDER')
#check if a custom geometry location has been specified
#if it has, add an ENV_VAR to handle it
if args.geometry:
geo_path = os.path.abspath(args.geometry)
if os.path.isdir(geo_path):
os.environ['PYGBE_GEOMETRY'] = geo_path
else:
sys.exit('Invalid geometry prefix provided (Folder not found)')
else:
geo_path = os.path.join(full_path, 'geometry')
#try to expand ~ if present in output path
args.output = os.path.expanduser(args.output)
#if output path is absolute, use that, otherwise prepend
#problem path
if not os.path.isdir(args.output):
output_dir = os.path.join(full_path, args.output)
else:
output_dir = args.output
#create output directory if it doesn't already exist
try:
os.makedirs(output_dir)
except OSError:
pass
results_dict = {}
timestamp = time.localtime()
outputfname = '{:%Y-%m-%d-%H%M%S}-output.log'.format(datetime.now())
results_dict['output_file'] = outputfname
if log_output:
sys.stdout = Logger(os.path.join(output_dir, outputfname))
### Time stamp
print 'Run started on:'
print '\tDate: %i/%i/%i' % (timestamp.tm_year, timestamp.tm_mon,
timestamp.tm_mday)
print '\tTime: %i:%i:%i' % (timestamp.tm_hour, timestamp.tm_min,
timestamp.tm_sec)
TIC = time.time()
print('Config file: {}'.format(configFile))
print('Parameter file: {}'.format(paramfile))
print('Geometry folder: {}'.format(geo_path))
print('Running in: {}'.format(full_path))
results_dict['config_file'] = configFile
results_dict['param_file'] = paramfile
results_dict['geo_file'] = geo_path
results_dict['full_path'] = full_path
### Read parameters
param = Parameters()
precision = readParameters(param, paramfile)
param.Nm = (param.P + 1) * (param.P + 2) * (
param.P + 3) / 6 # Number of terms in Taylor expansion
param.BlocksPerTwig = int(numpy.ceil(param.NCRIT / float(param.BSZ))
) # CUDA blocks that fit per twig
HAS_GPU = check_for_nvcc()
if param.GPU == 1 and not HAS_GPU:
print('\n\n\n\n')
print('{:-^{}}'.format('No GPU DETECTED', 60))
print("Your param file has `GPU = 1` but CUDA was not detected.\n"
"Continuing using CPU. If you do not want this, use Ctrl-C\n"
"to stop the program and check that your CUDA installation\n"
"is on your $PATH")
print('{:-^{}}'.format('No GPU DETECTED', 60))
print('\n\n\n\n')
param.GPU = 0
time.sleep(3)
### Generate array of fields
field_array = initializeField(configFile, param)
### Generate array of surfaces and read in elements
surf_array = initializeSurf(field_array, configFile, param)
### Fill surface class
time_sort = 0.
for i in range(len(surf_array)):
time_sort += fill_surface(surf_array[i], param)
### Output setup summary
param.N = 0
param.Neq = 0
for s in surf_array:
N_aux = len(s.triangle)
param.N += N_aux
if s.surf_type == 'dirichlet_surface' or s.surf_type == 'neumann_surface' or s.surf_type == 'asc_surface':
param.Neq += N_aux
else:
param.Neq += 2 * N_aux
print '\nTotal elements : %i' % param.N
print 'Total equations: %i' % param.Neq
results_dict['total_elements'] = param.N
results_dict['N_equation'] = param.Neq
results_dict = print_summary(surf_array, field_array, param, results_dict)
### Precomputation
ind0 = IndexConstant()
computeIndices(param.P, ind0)
precomputeTerms(param.P, ind0)
### Load CUDA code
if param.GPU == 1:
kernel = kernels(param.BSZ, param.Nm, param.K_fine, param.P, precision)
else:
kernel = 1
### Generate interaction list
print 'Generate interaction list'
tic = time.time()
generateList(surf_array, field_array, param)
toc = time.time()
list_time = toc - tic
### Transfer data to GPU
print 'Transfer data to GPU'
tic = time.time()
if param.GPU == 1:
dataTransfer(surf_array, field_array, ind0, param, kernel)
toc = time.time()
transfer_time = toc - tic
timing = Timing()
### Generate RHS
print 'Generate RHS'
tic = time.time()
if param.GPU == 0:
F = generateRHS(field_array, surf_array, param, kernel, timing, ind0)
elif param.GPU == 1:
F = generateRHS_gpu(field_array, surf_array, param, kernel, timing,
ind0)
toc = time.time()
rhs_time = toc - tic
setup_time = toc - TIC
print 'List time : %fs' % list_time
print 'Data transfer time : %fs' % transfer_time
print 'RHS generation time: %fs' % rhs_time
print '------------------------------'
print 'Total setup time : %fs\n' % setup_time
tic = time.time()
### Solve
print 'Solve'
phi = numpy.zeros(param.Neq)
phi = gmres_mgs(surf_array, field_array, phi, F, param, ind0, timing,
kernel)
toc = time.time()
solve_time = toc - tic
print 'Solve time : %fs' % solve_time
phifname = '{:%Y-%m-%d-%H%M%S}-phi.txt'.format(datetime.now())
results_dict['solve_time'] = solve_time
numpy.savetxt(os.path.join(output_dir, phifname), phi)
# Put result phi in corresponding surfaces
fill_phi(phi, surf_array)
### Calculate solvation energy
print '\nCalculate Esolv'
tic = time.time()
E_solv = calculateEsolv(surf_array, field_array, param, kernel)
toc = time.time()
print 'Time Esolv: %fs' % (toc - tic)
ii = -1
for f in param.E_field:
parent_type = surf_array[field_array[f].parent[0]].surf_type
if parent_type != 'dirichlet_surface' and parent_type != 'neumann_surface':
ii += 1
print 'Region %i: Esolv = %f kcal/mol = %f kJ/mol' % (
f, E_solv[ii], E_solv[ii] * 4.184)
results_dict['E_solv_kcal'] = E_solv[ii]
results_dict['E_solv_kJ'] = E_solv[ii] * 4.184
### Calculate surface energy
print '\nCalculate Esurf'
tic = time.time()
E_surf = calculateEsurf(surf_array, field_array, param, kernel)
toc = time.time()
ii = -1
for f in param.E_field:
parent_type = surf_array[field_array[f].parent[0]].surf_type
if parent_type == 'dirichlet_surface' or parent_type == 'neumann_surface':
ii += 1
print 'Region %i: Esurf = %f kcal/mol = %f kJ/mol' % (
f, E_surf[ii], E_surf[ii] * 4.184)
results_dict['E_surf_kcal'] = E_surf[ii]
results_dict['E_surf_kJ'] = E_surf[ii] * 4.184
print 'Time Esurf: %fs' % (toc - tic)
### Calculate Coulombic interaction
print '\nCalculate Ecoul'
tic = time.time()
i = -1
E_coul = []
for f in field_array:
i += 1
if f.coulomb == 1:
print 'Calculate Coulomb energy for region %i' % i
E_coul.append(coulombEnergy(f, param))
print 'Region %i: Ecoul = %f kcal/mol = %f kJ/mol' % (
i, E_coul[-1], E_coul[-1] * 4.184)
results_dict['E_coul_kcal'] = E_coul[-1]
results_dict['E_coul_kJ'] = E_coul[-1] * 4.184
toc = time.time()
print 'Time Ecoul: %fs' % (toc - tic)
### Output summary
print '\n--------------------------------'
print 'Totals:'
print 'Esolv = %f kcal/mol' % sum(E_solv)
print 'Esurf = %f kcal/mol' % sum(E_surf)
print 'Ecoul = %f kcal/mol' % sum(E_coul)
print '\nTime = %f s' % (toc - TIC)
results_dict['total_time'] = (toc - TIC)
output_pickle = outputfname.split('-')
output_pickle.pop(-1)
output_pickle.append('resultspickle')
output_pickle = '-'.join(output_pickle)
with open(os.path.join(output_dir, output_pickle), 'wb') as f:
pickle.dump(results_dict, f)
#reset stdout so regression tests, etc, don't get logged into the output
#file that they themselves are trying to read
sys.stdout = sys.__stdout__
if return_output_fname and log_output:
return outputfname
def main(argv=sys.argv,
log_output=True,
return_output_fname=False,
return_results_dict=False,
field=None):
"""
Run a PyGBe problem, write outputs to STDOUT and to log file in
problem directory
Arguments
----------
log_output : Bool, default True.
If False, output is written only to STDOUT and not to a log file.
return_output_fname: Bool, default False.
If True, function main() returns the name of the
output log file. This is used for the regression tests.
return_results_dict: Bool, default False.
If True, function main() returns the results of the run
packed in a dictionary. Used in testing and programmatic
use of PyGBe
field : Dictionary, defaults to None.
If passed, this dictionary will supercede any config file found, useful in
programmatically stepping through slight changes in a problem
Returns
--------
output_fname : str, if kwarg is True.
The name of the log file containing problem output
"""
args = read_inputs(argv[1:])
configFile, paramfile = find_config_files(args)
full_path = os.environ.get('PYGBE_PROBLEM_FOLDER')
#check if a custom geometry location has been specified
#if it has, add an ENV_VAR to handle it
if args.geometry:
geo_path = os.path.abspath(args.geometry)
if os.path.isdir(geo_path):
os.environ['PYGBE_GEOMETRY'] = geo_path
else:
sys.exit('Invalid geometry prefix provided (Folder not found)')
else:
geo_path = os.path.join(full_path, 'geometry')
#try to expand ~ if present in output path
args.output = os.path.expanduser(args.output)
#if output path is absolute, use that, otherwise prepend
#problem path
if not os.path.isdir(args.output):
output_dir = os.path.join(full_path, args.output)
else:
output_dir = args.output
# create output directory if it doesn't already exist
try:
os.makedirs(output_dir)
except OSError:
pass
results_dict = {}
timestamp = time.localtime()
outputfname = '{:%Y-%m-%d-%H%M%S}-output.log'.format(datetime.now())
results_dict['output_file'] = outputfname
if log_output:
restore_stdout = sys.stdout
sys.stdout = Logger(os.path.join(output_dir, outputfname))
# Time stamp
print('Run started on:')
print('\tDate: {}/{}/{}'.format(timestamp.tm_year, timestamp.tm_mon,
timestamp.tm_mday))
print('\tTime: {}:{}:{}'.format(timestamp.tm_hour, timestamp.tm_min,
timestamp.tm_sec))
print('\tPyGBe version: {}'.format(pygbe.__version__))
TIC = time.time()
print('Config file: {}'.format(configFile))
print('Parameter file: {}'.format(paramfile))
print('Geometry folder: {}'.format(geo_path))
print('Running in: {}'.format(full_path))
results_dict['config_file'] = configFile
results_dict['param_file'] = paramfile
results_dict['geo_file'] = geo_path
results_dict['full_path'] = full_path
### Read parameters
param = Parameters()
precision = read_parameters(param, paramfile)
param.Nm = (param.P + 1) * (param.P + 2) * (
param.P + 3) // 6 # Number of terms in Taylor expansion
param.BlocksPerTwig = int(numpy.ceil(
param.NCRIT / float(param.BSZ))) # CUDA blocks that fit per twig
HAS_GPU = check_for_nvcc()
if param.GPU == 1 and not HAS_GPU:
print('\n\n\n\n')
print('{:-^{}}'.format('No GPU DETECTED', 60))
print("Your param file has `GPU = 1` but CUDA was not detected.\n"
"Continuing using CPU. If you do not want this, use Ctrl-C\n"
"to stop the program and check that your CUDA installation\n"
"is on your $PATH")
print('{:-^{}}'.format('No GPU DETECTED', 60))
print('\n\n\n\n')
param.GPU = 0
### Generate array of fields
if field:
field_array = initialize_field(configFile, param, field)
else:
field_array = initialize_field(configFile, param)
### Generate array of surfaces and read in elements
surf_array = initialize_surface(field_array, configFile, param)
### Fill surface class
time_sort = 0.
for i in range(len(surf_array)):
time_sort += surf_array[i].fill_surface(param)
### Output setup summary
param.N = 0
param.Neq = 0
for s in surf_array:
N_aux = len(s.triangle)
param.N += N_aux
if s.surf_type in [
'dirichlet_surface', 'neumann_surface', 'asc_surface'
]:
param.Neq += N_aux
else:
param.Neq += 2 * N_aux
print('\nTotal elements : {}'.format(param.N))
print('Total equations: {}'.format(param.Neq))
results_dict['total_elements'] = param.N
results_dict['N_equation'] = param.Neq
results_dict = print_summary(surf_array, field_array, param, results_dict)
### Precomputation
ind0 = IndexConstant()
computeIndices(param.P, ind0)
precomputeTerms(param.P, ind0)
### Load CUDA code
if param.GPU == 1:
kernel = kernels(param.BSZ, param.Nm, param.K_fine, param.P, precision)
else:
kernel = 1
### Generate interaction list
print('Generate interaction list')
tic = time.time()
generateList(surf_array, field_array, param)
toc = time.time()
list_time = toc - tic
### Transfer data to GPU
print('Transfer data to GPU')
tic = time.time()
if param.GPU == 1:
dataTransfer(surf_array, field_array, ind0, param, kernel)
toc = time.time()
transfer_time = toc - tic
phi_sol = numpy.loadtxt(args.phi_file)
phi_vals = phi_sol[:len(surf_array[0].xi)]
dphi_vals = phi_sol[len(surf_array[0].xi):2 * len(surf_array[0].xi)]
dphir_x, dphir_y, dphir_z, AI = get_dphirdr_gpu(phi_vals, dphi_vals,
surf_array[0],
field_array[1], param,
kernel)
dphir = numpy.zeros((len(dphir_x), 3))
dphir[:, 0] = dphir_x[:]
dphir[:, 1] = dphir_y[:]
dphir[:, 2] = dphir_z[:]
# numpy.savetxt(args.phi_file[:-7]+"dphir_capsid.txt",dphir)
numpy.savetxt(args.phi_file[:-7] + "dphir.txt", dphir)