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ready for testing
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@MartinAchondo
MartinAchondo committed Jul 2, 2024
1 parent 1200bde commit fc033e6
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284 changes: 142 additions & 142 deletions tests/test_xppbe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,11 +59,11 @@ def test_scripts():
@pytest.mark.parametrize(
('pinns_method','model','scheme'),
(
#('DCM','linear','direct'),
('DCM','linear','direct'),
('DCM','linear', 'regularized_scheme_1'),
#('DCM','nonlinear','regularized_scheme_2'),
#('DVM','linear','direct'),
#('DVM','linear','regularized_scheme_1'),
('DCM','nonlinear','regularized_scheme_2'),
('DVM','linear','direct'),
('DVM','linear','regularized_scheme_1'),
('DVM','nonlinear','regularized_scheme_1'),
('DBM','linear','direct')
)
Expand All @@ -89,141 +89,141 @@ def test_pinns_method_and_schemes(pinns_method,model,scheme):
run_checkers(sim,sim_name,temp_dir)


# @pytest.mark.parametrize(
# ('molecule'),
# (
# ('methanol'),
# ('arg')
# )
# )
# def test_other_molecules(molecule):
# with tempfile.TemporaryDirectory() as temp_dir:
# sim_name = f'test_{molecule}'
# yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
# results_path = os.path.join(temp_dir,'results',sim_name)
# sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
# sim.create_simulation()
# sim.adapt_model()
# sim.solve_model()
# sim.postprocessing(run_all=True)
# run_checkers(sim,sim_name,temp_dir)


# def test_optimizers():
# with tempfile.TemporaryDirectory() as temp_dir:
# sim_name = f'test_optimizers'
# yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
# yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
# shutil.copy(yaml_prev_path,yaml_path)
# results_path = os.path.join(temp_dir,'results',sim_name)
# sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
# sim.options_optimizer2['maxiter'] = 3
# sim.N_steps_2 = 2
# sim.create_simulation()
# sim.adapt_model()
# sim.solve_model()
# sim.postprocessing(run_all=True)
# run_checkers(sim,sim_name,temp_dir,num_iters=2)


# @pytest.mark.parametrize(
# ('arch'),
# (
# ('ModMLP'),
# ('ResNet')
# )
# )
# def test_other_architectures(arch):
# with tempfile.TemporaryDirectory() as temp_dir:
# sim_name = f'test_{arch}'
# yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
# yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
# shutil.copy(yaml_prev_path,yaml_path)
# results_path = os.path.join(temp_dir,'results',sim_name)
# sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
# sim.hyperparameters_in['architecture_Net'] = arch
# sim.create_simulation()
# sim.adapt_model()
# sim.solve_model()
# sim.postprocessing(run_all=True)
# run_checkers(sim,sim_name,temp_dir)



# @pytest.mark.parametrize(
# ('loss'),
# (
# ('K2'),
# ('E2'),
# ('G')
# )
# )
# def test_additional_losses(loss):
# with tempfile.TemporaryDirectory() as temp_dir:
# sim_name = f'test_{loss}'
# yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
# yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
# shutil.copy(yaml_prev_path,yaml_path)
# results_path = os.path.join(temp_dir,'results',sim_name)
# sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
# sim.losses.append(loss)
# if loss == 'E2':
# sim.mesh_properties['dR_exterior'] = 5
# sim.create_simulation()
# sim.adapt_model()
# sim.solve_model()
# sim.postprocessing(run_all=True)
# run_checkers(sim,sim_name,temp_dir)


# def test_mesh_post():
# with tempfile.TemporaryDirectory() as temp_dir:
# sim_name = f'test_mesh_post'
# yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
# yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
# shutil.copy(yaml_prev_path,yaml_path)
# results_path = os.path.join(temp_dir,'results',sim_name)
# sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
# sim.create_simulation()
# sim.adapt_model()
# sim.solve_model()
# sim.postprocessing(run_all=True, plot_mesh=True)
# run_checkers(sim,sim_name,temp_dir)


# def test_iteration_continuation():
# with tempfile.TemporaryDirectory() as temp_dir:
# sim_name = 'test_iteration'
# yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
# yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
# shutil.copy(yaml_prev_path,yaml_path)
# results_path = os.path.join(temp_dir,'results',sim_name)
# sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
# sim.create_simulation()
# sim.adapt_model()
# sim.solve_model()
# sim.postprocessing(run_all=True)

# assert os.path.isdir(results_path)
# assert len(os.listdir(results_path)) > 0

# iterations_path = os.path.join(results_path,'iterations')
# assert len(os.listdir(iterations_path)) == 1

# sim_2 = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
# sim_2.N_iters = sim.N_iters*2
# sim_2.create_simulation()
# sim_2.adapt_model()
# sim_2.solve_model()
# sim_2.postprocessing(run_all=True)

# last_iteration = os.path.join(iterations_path,f'iter_{sim_2.N_iters}')

# for file_name in ['loss.csv','loss_validation.csv','w_hist.csv','G_solv.csv']:
# file = os.path.join(last_iteration,file_name)
# with open(file, 'r') as csvfile:
# reader = csv.reader(csvfile)
# lines = list(reader)
# assert len(lines) == sim.N_iters*2 + 1
# last_line = lines[-1]
# assert not '' in last_line
@pytest.mark.parametrize(
('molecule'),
(
('methanol'),
('arg')
)
)
def test_other_molecules(molecule):
with tempfile.TemporaryDirectory() as temp_dir:
sim_name = f'test_{molecule}'
yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
results_path = os.path.join(temp_dir,'results',sim_name)
sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
sim.create_simulation()
sim.adapt_model()
sim.solve_model()
sim.postprocessing(run_all=True)
run_checkers(sim,sim_name,temp_dir)


def test_optimizers():
with tempfile.TemporaryDirectory() as temp_dir:
sim_name = f'test_optimizers'
yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
shutil.copy(yaml_prev_path,yaml_path)
results_path = os.path.join(temp_dir,'results',sim_name)
sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
sim.options_optimizer2['maxiter'] = 3
sim.N_steps_2 = 2
sim.create_simulation()
sim.adapt_model()
sim.solve_model()
sim.postprocessing(run_all=True)
run_checkers(sim,sim_name,temp_dir,num_iters=2)


@pytest.mark.parametrize(
('arch'),
(
('ModMLP'),
('ResNet')
)
)
def test_other_architectures(arch):
with tempfile.TemporaryDirectory() as temp_dir:
sim_name = f'test_{arch}'
yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
shutil.copy(yaml_prev_path,yaml_path)
results_path = os.path.join(temp_dir,'results',sim_name)
sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
sim.hyperparameters_in['architecture_Net'] = arch
sim.create_simulation()
sim.adapt_model()
sim.solve_model()
sim.postprocessing(run_all=True)
run_checkers(sim,sim_name,temp_dir)



@pytest.mark.parametrize(
('loss'),
(
('K2'),
('E2'),
('G')
)
)
def test_additional_losses(loss):
with tempfile.TemporaryDirectory() as temp_dir:
sim_name = f'test_{loss}'
yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
shutil.copy(yaml_prev_path,yaml_path)
results_path = os.path.join(temp_dir,'results',sim_name)
sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
sim.losses.append(loss)
if loss == 'E2':
sim.mesh_properties['dR_exterior'] = 5
sim.create_simulation()
sim.adapt_model()
sim.solve_model()
sim.postprocessing(run_all=True)
run_checkers(sim,sim_name,temp_dir)


def test_mesh_post():
with tempfile.TemporaryDirectory() as temp_dir:
sim_name = f'test_mesh_post'
yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
shutil.copy(yaml_prev_path,yaml_path)
results_path = os.path.join(temp_dir,'results',sim_name)
sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
sim.create_simulation()
sim.adapt_model()
sim.solve_model()
sim.postprocessing(run_all=True, plot_mesh=True)
run_checkers(sim,sim_name,temp_dir)


def test_iteration_continuation():
with tempfile.TemporaryDirectory() as temp_dir:
sim_name = 'test_iteration'
yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
yaml_prev_path = os.path.join(os.path.dirname(__file__),'simulations_yaml','test_born_ion.yaml')
shutil.copy(yaml_prev_path,yaml_path)
results_path = os.path.join(temp_dir,'results',sim_name)
sim = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
sim.create_simulation()
sim.adapt_model()
sim.solve_model()
sim.postprocessing(run_all=True)

assert os.path.isdir(results_path)
assert len(os.listdir(results_path)) > 0

iterations_path = os.path.join(results_path,'iterations')
assert len(os.listdir(iterations_path)) == 1

sim_2 = Simulation(yaml_path, results_path=results_path, molecule_dir=None)
sim_2.N_iters = sim.N_iters*2
sim_2.create_simulation()
sim_2.adapt_model()
sim_2.solve_model()
sim_2.postprocessing(run_all=True)

last_iteration = os.path.join(iterations_path,f'iter_{sim_2.N_iters}')

for file_name in ['loss.csv','loss_validation.csv','w_hist.csv','G_solv.csv']:
file = os.path.join(last_iteration,file_name)
with open(file, 'r') as csvfile:
reader = csv.reader(csvfile)
lines = list(reader)
assert len(lines) == sim.N_iters*2 + 1
last_line = lines[-1]
assert not '' in last_line
12 changes: 6 additions & 6 deletions xppbe/Model/Solutions_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,9 +139,9 @@ def dG_L(self,X,Xp,N):
# Compute the derivative of the Green's function with respect to r
dg_dr = (-1 / (4 * self.pi)) / (r**2) # Shape: (n, m)
# Compute the components of the gradient
grad_x = dg_dr * r_diff[:, :, 0] / r # Shape: (n, m)
grad_y = dg_dr * r_diff[:, :, 1] / r # Shape: (n, m)
grad_z = dg_dr * r_diff[:, :, 2] / r # Shape: (n, m)
grad_x = -1*dg_dr * r_diff[:, :, 0] / r # Shape: (n, m)
grad_y = -1*dg_dr * r_diff[:, :, 1] / r # Shape: (n, m)
grad_z = -1*dg_dr * r_diff[:, :, 2] / r # Shape: (n, m)
# Combine the components into the gradient
grad = tf.stack([grad_x, grad_y, grad_z], axis=2) # Shape: (n, m, 3)
# Compute the dot product of the gradient with the normal vector
Expand All @@ -159,9 +159,9 @@ def dG_Y(self,X,Xp,N):
# Compute the derivative of the Green's function with respect to r
dg_dr = (-tf.exp(-self.kappa*r) / (4 * self.pi)) / (r) *(-self.kappa/r - 1/r**2) # Shape: (n, m)
# Compute the components of the gradient
grad_x = dg_dr * r_diff[:, :, 0] / r # Shape: (n, m)
grad_y = dg_dr * r_diff[:, :, 1] / r # Shape: (n, m)
grad_z = dg_dr * r_diff[:, :, 2] / r # Shape: (n, m)
grad_x = -1*dg_dr * r_diff[:, :, 0] / r # Shape: (n, m)
grad_y = -1*dg_dr * r_diff[:, :, 1] / r # Shape: (n, m)
grad_z = -1*dg_dr * r_diff[:, :, 2] / r # Shape: (n, m)
# Combine the components into the gradient
grad = tf.stack([grad_x, grad_y, grad_z], axis=2) # Shape: (n, m, 3)
# Compute the dot product of the gradient with the normal vector
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