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!18192 0611 sponge case 

Merge pull request !18192 from jiahongQian/master
This commit is contained in:
i-robot 2021-06-15 14:45:41 +08:00 committed by Gitee
parent f2c7a47714 baaa281df6
commit 4d984fab6a
1 changed files with 40 additions and 89 deletions
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129
model_zoo/research/hpc/sponge/src/simulation.py
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@ -122,6 +122,8 @@ class Simulation(nn.Cell):
self.init_Tensor() self.init_Tensor()
self.op_define() self.op_define()
self.update = False self.update = False
self.file = None
self.datfile = None
def init_Tensor(self): def init_Tensor(self):
'''init tensor''' '''init tensor'''
@ -406,97 +408,46 @@ class Simulation(nn.Cell):
def construct(self, step, print_step): def construct(self, step, print_step):
'''construct''' '''construct'''
self.last_crd = self.crd self.last_crd = self.crd
if step == 0: res = self.neighbor_list_update(self.atom_numbers_in_grid_bucket,
res = self.neighbor_list_update_init(self.atom_numbers_in_grid_bucket, self.bucket, self.crd, self.bucket,
self.box_length, self.grid_N, self.grid_length_inverse, self.crd,
self.atom_in_grid_serial, self.old_crd, self.crd_to_uint_crd_cof, self.box_length,
self.uint_crd, self.pointer, self.nl_atom_numbers, self.nl_atom_serial, self.grid_N,
self.uint_dr_to_dr_cof, self.excluded_list_start, self.excluded_list, self.grid_length_inverse,
self.excluded_numbers, self.need_refresh_flag, self.refresh_count) self.atom_in_grid_serial,
self.nl_atom_numbers = F.depend(self.nl_atom_numbers, res) self.old_crd,
self.nl_atom_serial = F.depend(self.nl_atom_serial, res) self.crd_to_uint_crd_cof,
self.uint_dr_to_dr_cof = F.depend(self.uint_dr_to_dr_cof, res) self.uint_crd,
self.old_crd = F.depend(self.old_crd, res) self.pointer,
self.atom_numbers_in_grid_bucket = F.depend(self.atom_numbers_in_grid_bucket, res) self.nl_atom_numbers,
self.bucket = F.depend(self.bucket, res) self.nl_atom_serial,
self.atom_in_grid_serial = F.depend(self.atom_in_grid_serial, res) self.uint_dr_to_dr_cof,
self.pointer = F.depend(self.pointer, res) self.excluded_list_start,
uint_crd = F.depend(self.uint_crd, res) self.excluded_list,
self.excluded_numbers,
force = self.Simulation_Caculate_Force(uint_crd, self.uint_dr_to_dr_cof, self.nl_atom_numbers, self.need_refresh_flag,
self.nl_atom_serial) self.refresh_count)
uint_crd = self.Simulation_Beforce_Caculate_Force()
force = self.Simulation_Caculate_Force(uint_crd, self.uint_dr_to_dr_cof, self.nl_atom_numbers,
self.nl_atom_serial)
if print_step == 0:
bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, nb14_cf_energy_sum, \ bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, nb14_cf_energy_sum, \
lj_energy_sum, ee_ene, total_energy = self.Simulation_Caculate_Energy(uint_crd, self.uint_dr_to_dr_cof) lj_energy_sum, ee_ene, total_energy = self.Simulation_Caculate_Energy(uint_crd, self.uint_dr_to_dr_cof)
temperature = self.Simulation_Temperature()
self.rand_state = self.setup_random_state()
self.velocity, self.crd, _ = self.Simulation_MDIterationLeapFrog_Liujian(self.mass_inverse,
self.sqrt_mass, self.crd, force,
self.rand_state,
self.random_force)
res = self.neighbor_list_update(self.atom_numbers_in_grid_bucket,
self.bucket,
self.crd,
self.box_length,
self.grid_N,
self.grid_length_inverse,
self.atom_in_grid_serial,
self.old_crd,
self.crd_to_uint_crd_cof,
self.uint_crd,
self.pointer,
self.nl_atom_numbers,
self.nl_atom_serial,
self.uint_dr_to_dr_cof,
self.excluded_list_start,
self.excluded_list,
self.excluded_numbers,
self.need_refresh_flag,
self.refresh_count)
self.nl_atom_numbers = F.depend(self.nl_atom_numbers, res)
self.nl_atom_serial = F.depend(self.nl_atom_serial, res)
else: else:
uint_crd = self.Simulation_Beforce_Caculate_Force() bond_energy_sum = self.zero_fp_tensor
force = self.Simulation_Caculate_Force(uint_crd, self.uint_dr_to_dr_cof, self.nl_atom_numbers, angle_energy_sum = self.zero_fp_tensor
self.nl_atom_serial) dihedral_energy_sum = self.zero_fp_tensor
if print_step == 0: nb14_lj_energy_sum = self.zero_fp_tensor
bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, nb14_cf_energy_sum, \ nb14_cf_energy_sum = self.zero_fp_tensor
lj_energy_sum, ee_ene, total_energy = self.Simulation_Caculate_Energy( lj_energy_sum = self.zero_fp_tensor
uint_crd, self.uint_dr_to_dr_cof) ee_ene = self.zero_fp_tensor
else: total_energy = self.zero_fp_tensor
bond_energy_sum = self.zero_fp_tensor temperature = self.Simulation_Temperature()
angle_energy_sum = self.zero_fp_tensor if step == 0:
dihedral_energy_sum = self.zero_fp_tensor self.rand_state = self.setup_random_state()
nb14_lj_energy_sum = self.zero_fp_tensor self.velocity, self.crd, _ = self.Simulation_MDIterationLeapFrog_Liujian(self.mass_inverse,
nb14_cf_energy_sum = self.zero_fp_tensor self.sqrt_mass, self.crd, force,
lj_energy_sum = self.zero_fp_tensor self.rand_state,
ee_ene = self.zero_fp_tensor self.random_force)
total_energy = self.zero_fp_tensor
temperature = self.Simulation_Temperature()
self.velocity, self.crd, _ = self.Simulation_MDIterationLeapFrog_Liujian(self.mass_inverse,
self.sqrt_mass, self.crd, force,
self.rand_state,
self.random_force)
res = self.neighbor_list_update(self.atom_numbers_in_grid_bucket,
self.bucket,
self.crd,
self.box_length,
self.grid_N,
self.grid_length_inverse,
self.atom_in_grid_serial,
self.old_crd,
self.crd_to_uint_crd_cof,
self.uint_crd,
self.pointer,
self.nl_atom_numbers,
self.nl_atom_serial,
self.uint_dr_to_dr_cof,
self.excluded_list_start,
self.excluded_list,
self.excluded_numbers,
self.need_refresh_flag,
self.refresh_count)
self.nl_atom_numbers = F.depend(self.nl_atom_numbers, res)
self.nl_atom_serial = F.depend(self.nl_atom_serial, res)
return temperature, total_energy, bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, \ return temperature, total_energy, bond_energy_sum, angle_energy_sum, dihedral_energy_sum, nb14_lj_energy_sum, \
nb14_cf_energy_sum, lj_energy_sum, ee_ene, res nb14_cf_energy_sum, lj_energy_sum, ee_ene, res