!18192 0611 sponge case
Merge pull request !18192 from jiahongQian/master
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@ -122,6 +122,8 @@ class Simulation(nn.Cell):
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self.init_Tensor()
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self.op_define()
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self.update = False
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self.file = None
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self.datfile = None
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def init_Tensor(self):
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'''init tensor'''
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@ -406,97 +408,46 @@ class Simulation(nn.Cell):
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def construct(self, step, print_step):
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'''construct'''
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self.last_crd = self.crd
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if step == 0:
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res = self.neighbor_list_update_init(self.atom_numbers_in_grid_bucket, self.bucket, self.crd,
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self.box_length, self.grid_N, self.grid_length_inverse,
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self.atom_in_grid_serial, self.old_crd, self.crd_to_uint_crd_cof,
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self.uint_crd, self.pointer, self.nl_atom_numbers, self.nl_atom_serial,
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self.uint_dr_to_dr_cof, self.excluded_list_start, self.excluded_list,
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self.excluded_numbers, self.need_refresh_flag, self.refresh_count)
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self.nl_atom_numbers = F.depend(self.nl_atom_numbers, res)
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self.nl_atom_serial = F.depend(self.nl_atom_serial, res)
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self.uint_dr_to_dr_cof = F.depend(self.uint_dr_to_dr_cof, res)
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self.old_crd = F.depend(self.old_crd, res)
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self.atom_numbers_in_grid_bucket = F.depend(self.atom_numbers_in_grid_bucket, res)
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self.bucket = F.depend(self.bucket, res)
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self.atom_in_grid_serial = F.depend(self.atom_in_grid_serial, res)
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self.pointer = F.depend(self.pointer, res)
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uint_crd = F.depend(self.uint_crd, res)
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force = self.Simulation_Caculate_Force(uint_crd, self.uint_dr_to_dr_cof, self.nl_atom_numbers,
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self.nl_atom_serial)
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res = self.neighbor_list_update(self.atom_numbers_in_grid_bucket,
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self.bucket,
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self.crd,
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self.box_length,
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self.grid_N,
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self.grid_length_inverse,
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self.atom_in_grid_serial,
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self.old_crd,
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self.crd_to_uint_crd_cof,
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self.uint_crd,
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self.pointer,
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self.nl_atom_numbers,
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self.nl_atom_serial,
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self.uint_dr_to_dr_cof,
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self.excluded_list_start,
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self.excluded_list,
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self.excluded_numbers,
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self.need_refresh_flag,
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self.refresh_count)
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uint_crd = self.Simulation_Beforce_Caculate_Force()
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force = self.Simulation_Caculate_Force(uint_crd, self.uint_dr_to_dr_cof, self.nl_atom_numbers,
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self.nl_atom_serial)
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if print_step == 0:
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bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, nb14_cf_energy_sum, \
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lj_energy_sum, ee_ene, total_energy = self.Simulation_Caculate_Energy(uint_crd, self.uint_dr_to_dr_cof)
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temperature = self.Simulation_Temperature()
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self.rand_state = self.setup_random_state()
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self.velocity, self.crd, _ = self.Simulation_MDIterationLeapFrog_Liujian(self.mass_inverse,
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self.sqrt_mass, self.crd, force,
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self.rand_state,
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self.random_force)
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res = self.neighbor_list_update(self.atom_numbers_in_grid_bucket,
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self.bucket,
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self.crd,
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self.box_length,
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self.grid_N,
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self.grid_length_inverse,
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self.atom_in_grid_serial,
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self.old_crd,
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self.crd_to_uint_crd_cof,
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self.uint_crd,
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self.pointer,
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self.nl_atom_numbers,
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self.nl_atom_serial,
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self.uint_dr_to_dr_cof,
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self.excluded_list_start,
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self.excluded_list,
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self.excluded_numbers,
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self.need_refresh_flag,
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self.refresh_count)
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self.nl_atom_numbers = F.depend(self.nl_atom_numbers, res)
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self.nl_atom_serial = F.depend(self.nl_atom_serial, res)
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else:
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uint_crd = self.Simulation_Beforce_Caculate_Force()
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force = self.Simulation_Caculate_Force(uint_crd, self.uint_dr_to_dr_cof, self.nl_atom_numbers,
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self.nl_atom_serial)
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if print_step == 0:
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bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, nb14_cf_energy_sum, \
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lj_energy_sum, ee_ene, total_energy = self.Simulation_Caculate_Energy(
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uint_crd, self.uint_dr_to_dr_cof)
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else:
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bond_energy_sum = self.zero_fp_tensor
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angle_energy_sum = self.zero_fp_tensor
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dihedral_energy_sum = self.zero_fp_tensor
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nb14_lj_energy_sum = self.zero_fp_tensor
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nb14_cf_energy_sum = self.zero_fp_tensor
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lj_energy_sum = self.zero_fp_tensor
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ee_ene = self.zero_fp_tensor
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total_energy = self.zero_fp_tensor
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temperature = self.Simulation_Temperature()
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self.velocity, self.crd, _ = self.Simulation_MDIterationLeapFrog_Liujian(self.mass_inverse,
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self.sqrt_mass, self.crd, force,
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self.rand_state,
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self.random_force)
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res = self.neighbor_list_update(self.atom_numbers_in_grid_bucket,
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self.bucket,
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self.crd,
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self.box_length,
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self.grid_N,
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self.grid_length_inverse,
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self.atom_in_grid_serial,
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self.old_crd,
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self.crd_to_uint_crd_cof,
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self.uint_crd,
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self.pointer,
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self.nl_atom_numbers,
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self.nl_atom_serial,
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self.uint_dr_to_dr_cof,
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self.excluded_list_start,
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self.excluded_list,
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self.excluded_numbers,
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self.need_refresh_flag,
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self.refresh_count)
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self.nl_atom_numbers = F.depend(self.nl_atom_numbers, res)
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self.nl_atom_serial = F.depend(self.nl_atom_serial, res)
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bond_energy_sum = self.zero_fp_tensor
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angle_energy_sum = self.zero_fp_tensor
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dihedral_energy_sum = self.zero_fp_tensor
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nb14_lj_energy_sum = self.zero_fp_tensor
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nb14_cf_energy_sum = self.zero_fp_tensor
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lj_energy_sum = self.zero_fp_tensor
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ee_ene = self.zero_fp_tensor
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total_energy = self.zero_fp_tensor
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temperature = self.Simulation_Temperature()
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if step == 0:
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self.rand_state = self.setup_random_state()
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self.velocity, self.crd, _ = self.Simulation_MDIterationLeapFrog_Liujian(self.mass_inverse,
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self.sqrt_mass, self.crd, force,
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self.rand_state,
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self.random_force)
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return temperature, total_energy, bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, \
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nb14_cf_energy_sum, lj_energy_sum, ee_ene, res
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