forked from mindspore-Ecosystem/mindspore
!13811 fix sponge ops
From: @jiahongqian Reviewed-by: @wang_zi_dong,@ljl0711,@wang_zi_dong Signed-off-by: @ljl0711
This commit is contained in:
Gitee
commit
2e7f9efebd
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@ -23,11 +23,8 @@ from ...common import dtype as mstype
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class BondForce(PrimitiveWithInfer):
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"""
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BondForce:
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Calculate the force exerted by the simple harmonic bond on the
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corresponding atoms. Assume the number of harmonic bonds is M and
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the number of atoms is N.
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Calculate the force exerted by the simple harmonic bond on the corresponding atoms.
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Assume the number of harmonic bonds is M and the number of atoms is N.
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.. math::
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@ -90,8 +87,6 @@ class BondForce(PrimitiveWithInfer):
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class BondEnergy(PrimitiveWithInfer):
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"""
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BondEnergy:
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Calculate the harmonic potential energy between each bonded atom pair.
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Assume our system has N atoms and M harmonic bonds.
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@ -101,15 +96,17 @@ class BondEnergy(PrimitiveWithInfer):
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E = k*(|dr| - r_0)^2
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Args:
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Same as operator BondForce().
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atom_numbers(int32): the number of atoms N.
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bond_numbers(int32): the number of harmonic bonds M.
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Inputs:
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Same as operator BondForce().
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.. math::
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dr = (x_1-x_2, y_1-y_2, z_1-z_2)
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E = k*(|dr| - r_0)^2
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- **uint_crd_f** (Tensor, uint32 ) - [N, 3], the unsigned int coordinate value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor (x, y, z),
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between the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the first atom index of each bond.
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- **atom_b** (Tensor, int32) - [M,], the second atom index of each bond.
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- **bond_k** (Tensor, float32) - [M,], the force constant of each bond.
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- **bond_r0** (Tensor, float32) - [M,], the equlibrium length of each bond.
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Outputs:
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- **bond_ene** (Tensor, float32) - [M,], the harmonic potential energy for each bond.
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@ -155,18 +152,23 @@ class BondEnergy(PrimitiveWithInfer):
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class BondAtomEnergy(PrimitiveWithInfer):
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"""
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BondAtomEnergy:
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Add the potential energy caused by simple harmonic bonds to the total
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potential energy of each atom.
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The calculation formula is the same as operator BondEnergy().
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Args:
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Same as operator BondForce().
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atom_numbers(int32): the number of atoms N.
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bond_numbers(int32): the number of harmonic bonds M.
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Inputs:
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Same as operator BondForce().
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- **uint_crd_f** (Tensor, uint32 ) - [N, 3], the unsigned int coordinate value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor (x, y, z),
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between the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the first atom index of each bond.
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- **atom_b** (Tensor, int32) - [M,], the second atom index of each bond.
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- **bond_k** (Tensor, float32) - [M,], the force constant of each bond.
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- **bond_r0** (Tensor, float32) - [M,], the equlibrium length of each bond.
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Outputs:
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- **atom_ene** (Tensor, float32) - [N,], the accumulated potential energy for each atom.
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@ -211,17 +213,22 @@ class BondAtomEnergy(PrimitiveWithInfer):
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class BondForceWithAtomEnergy(PrimitiveWithInfer):
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"""
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BondForceWithAtomEnergy:
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Calculate bond force and harmonic potential energy together.
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The calculation formula is the same as operator BondForce() and BondEnergy().
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Args:
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Same as operator BondForce().
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atom_numbers(int32): the number of atoms N.
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bond_numbers(int32): the number of harmonic bonds M.
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Inputs:
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Same as operator BondForce().
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- **uint_crd_f** (Tensor, uint32 ) - [N, 3], the unsigned int coordinate value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor (x, y, z),
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between the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the first atom index of each bond.
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- **atom_b** (Tensor, int32) - [M,], the second atom index of each bond.
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- **bond_k** (Tensor, float32) - [M,], the force constant of each bond.
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- **bond_r0** (Tensor, float32) - [M,], the equlibrium length of each bond.
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Outputs:
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- **frc_f** (Tensor, float32) - [N, 3], same as operator BondForce().
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@ -270,8 +277,6 @@ class BondForceWithAtomEnergy(PrimitiveWithInfer):
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class BondForceWithAtomVirial(PrimitiveWithInfer):
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"""
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BondForceWithAtomVirial:
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Calculate bond force and the virial coefficient caused by simple harmonic
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bond for each atom together.
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@ -284,10 +289,17 @@ class BondForceWithAtomVirial(PrimitiveWithInfer):
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virial = |dr|*(|dr| - r_0)*k
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Args:
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Same as operator BondForce().
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atom_numbers(int32): the number of atoms N.
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bond_numbers(int32): the number of harmonic bonds M.
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Inputs:
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Same as operator BondForce()
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- **uint_crd_f** (Tensor, uint32 ) - [N, 3], the unsigned int coordinate value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor (x, y, z),
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between the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the first atom index of each bond.
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- **atom_b** (Tensor, int32) - [M,], the second atom index of each bond.
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- **bond_k** (Tensor, float32) - [M,], the force constant of each bond.
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- **bond_r0** (Tensor, float32) - [M,], the equlibrium length of each bond.
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Outputs:
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- **frc_f** (Tensor, float32) - [N, 3], same as operator BondForce().
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@ -336,8 +348,6 @@ class BondForceWithAtomVirial(PrimitiveWithInfer):
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class DihedralForce(PrimitiveWithInfer):
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"""
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DihedralForce:
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Calculate the force exerted by the dihedral term which made of 4-atoms
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on the corresponding atoms. Assume the number of dihedral terms is M and
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the number of atoms is N.
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@ -438,8 +448,6 @@ class DihedralForce(PrimitiveWithInfer):
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class DihedralEnergy(PrimitiveWithInfer):
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"""
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DihedralEnergy:
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Calculate the potential energy caused by dihedral terms for each 4-atom pair.
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Assume our system has N atoms and M dihedral terms.
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@ -448,10 +456,24 @@ class DihedralEnergy(PrimitiveWithInfer):
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E = k(1 + cos(n*phi - phi_0))
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Args:
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Same as operator DihedralForce().
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dihedral_numbers(int32): the number of dihedral terms M.
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Inputs:
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Same as operator DihedralForce().
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- **dihedral_numbers** (int32) - the number of dihedral terms M.
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- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinates
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value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor between
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the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the 1st atom index of each dihedral.
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- **atom_b** (Tensor, int32) - [M,], the 2nd atom index of each dihedral.
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- **atom_c** (Tensor, int32) - [M,], the 3rd atom index of each dihedral.
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- **atom_d** (Tensor, int32) - [M,], the 4th atom index of each dihedral.
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4 atoms are connected in the form a-b-c-d.
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- **ipn** (Tensor, int32) - [M,], the period of dihedral angle of each dihedral.
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- **pk** (Tensor, float32) - [M,], the force constant of each dihedral.
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- **gamc** (Tensor, float32) - [M,], k*cos(phi_0) of each dihedral.
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- **gams** (Tensor, float32) - [M,], k*sin(phi_0) of each dihedral.
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- **pn** (Tensor, float32) - [M,], the floating point form of ipn.
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Outputs:
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- **ene** (Tensor, float32) - [M,], the potential energy for each
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@ -506,18 +528,30 @@ class DihedralEnergy(PrimitiveWithInfer):
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class DihedralAtomEnergy(PrimitiveWithInfer):
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"""
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DihedralAtomEnergy:
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Add the potential energy caused by dihedral terms to the total potential
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energy of each atom.
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The calculation formula is the same as operator DihedralEnergy().
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Args:
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Same as operator DihedralEnergy().
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dihedral_numbers(int32): the number of dihedral terms M.
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Inputs:
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Same as operator DihedralEnergy().
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- **dihedral_numbers** (int32) - the number of dihedral terms M.
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- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinates
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value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor between
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the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the 1st atom index of each dihedral.
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- **atom_b** (Tensor, int32) - [M,], the 2nd atom index of each dihedral.
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- **atom_c** (Tensor, int32) - [M,], the 3rd atom index of each dihedral.
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- **atom_d** (Tensor, int32) - [M,], the 4th atom index of each dihedral.
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4 atoms are connected in the form a-b-c-d.
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- **ipn** (Tensor, int32) - [M,], the period of dihedral angle of each dihedral.
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- **pk** (Tensor, float32) - [M,], the force constant of each dihedral.
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- **gamc** (Tensor, float32) - [M,], k*cos(phi_0) of each dihedral.
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- **gams** (Tensor, float32) - [M,], k*sin(phi_0) of each dihedral.
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- **pn** (Tensor, float32) - [M,], the floating point form of ipn.
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Outputs:
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- **ene** (Tensor, float32) - [N,], the accumulated potential
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@ -573,17 +607,29 @@ class DihedralAtomEnergy(PrimitiveWithInfer):
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class DihedralForceWithAtomEnergy(PrimitiveWithInfer):
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"""
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DihedralForceWithAtomEnergy:
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Calculate dihedral force and potential energy together.
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The calculation formula is the same as operator DihedralForce() and DihedralEnergy().
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Args:
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Same as operator DihedralForce().
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dihedral_numbers(int32): the number of dihedral terms M.
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Inputs:
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Same as operator DihedralForce().
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- **dihedral_numbers** (int32) - the number of dihedral terms M.
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- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinates
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value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor between
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the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the 1st atom index of each dihedral.
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- **atom_b** (Tensor, int32) - [M,], the 2nd atom index of each dihedral.
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- **atom_c** (Tensor, int32) - [M,], the 3rd atom index of each dihedral.
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- **atom_d** (Tensor, int32) - [M,], the 4th atom index of each dihedral.
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4 atoms are connected in the form a-b-c-d.
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- **ipn** (Tensor, int32) - [M,], the period of dihedral angle of each dihedral.
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- **pk** (Tensor, float32) - [M,], the force constant of each dihedral.
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- **gamc** (Tensor, float32) - [M,], k*cos(phi_0) of each dihedral.
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- **gams** (Tensor, float32) - [M,], k*sin(phi_0) of each dihedral.
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- **pn** (Tensor, float32) - [M,], the floating point form of ipn.
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Outputs:
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- **frc_f** (Tensor, float32) - [N, 3], same as operator DihedralForce().
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@ -639,8 +685,6 @@ class DihedralForceWithAtomEnergy(PrimitiveWithInfer):
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class AngleForce(PrimitiveWithInfer):
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"""
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AngleForce:
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Calculate the force exerted by angles made of 3 atoms on the
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corresponding atoms. Assume the number of angles is M and the
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number of atoms is N.
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@ -712,8 +756,6 @@ class AngleForce(PrimitiveWithInfer):
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class AngleEnergy(PrimitiveWithInfer):
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"""
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AngleEnergy:
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Calculate the energy caused by 3-atoms angle term.
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.. math::
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@ -724,10 +766,17 @@ class AngleEnergy(PrimitiveWithInfer):
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E = k*(theta - theta_0)^2
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Args:
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Same as operator AngleForce().
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angle_numbers(int32): the number of angles M.
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Inputs:
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Same as operator AngleForce().
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- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor between
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the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the 1st atom index of each angle.
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- **atom_b** (Tensor, int32) - [M,], the 2nd and the central atom index of each angle.
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- **atom_c** (Tensor, int32) - [M,], the 3rd atom index of each angle.
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- **angle_k** (Tensor, float32) - [M,], the force constant for each angle.
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- **angle_theta0** (Tensor, float32) - [M,], the equilibrium position value for each angle.
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Outputs:
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- **ene** (Tensor, float32) - [M,], the potential energy for each angle term.
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@ -772,18 +821,23 @@ class AngleEnergy(PrimitiveWithInfer):
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class AngleAtomEnergy(PrimitiveWithInfer):
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"""
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AngleAtomEnergy:
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Add the potential energy caused by angle terms to the total potential
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energy of each atom.
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The calculation formula is the same as operator AngleEnergy().
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Args:
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Same as operator AngleForce().
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angle_numbers(int32): the number of angles M.
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Inputs:
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Same as operator AngleForce().
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- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor between
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the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the 1st atom index of each angle.
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- **atom_b** (Tensor, int32) - [M,], the 2nd and the central atom index of each angle.
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- **atom_c** (Tensor, int32) - [M,], the 3rd atom index of each angle.
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- **angle_k** (Tensor, float32) - [M,], the force constant for each angle.
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- **angle_theta0** (Tensor, float32) - [M,], the equilibrium position value for each angle.
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Outputs:
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- **ene** (Tensor, float32) - [N,], the accumulated potential energy for each atom.
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@ -829,17 +883,22 @@ class AngleAtomEnergy(PrimitiveWithInfer):
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class AngleForceWithAtomEnergy(PrimitiveWithInfer):
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"""
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AngleForceWithAtomEnergy:
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Calculate angle force and potential energy together.
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The calculation formula is the same as operator AngleForce() and AngleEnergy().
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Args:
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Same as operator AngleForce().
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angle_numbers(int32): the number of angles M.
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Inputs:
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Same as operator AngleForce().
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- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
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- **scaler_f** (Tensor, float32) - [3,], the 3-D scale factor between
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the real space float coordinates and the unsigned int coordinates.
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- **atom_a** (Tensor, int32) - [M,], the 1st atom index of each angle.
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- **atom_b** (Tensor, int32) - [M,], the 2nd and the central atom index of each angle.
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- **atom_c** (Tensor, int32) - [M,], the 3rd atom index of each angle.
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- **angle_k** (Tensor, float32) - [M,], the force constant for each angle.
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- **angle_theta0** (Tensor, float32) - [M,], the equilibrium position value for each angle.
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Outputs:
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- **frc_f** (Tensor, float32) - [N, 3], same as operator AngleForce().
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@ -886,11 +945,10 @@ class AngleForceWithAtomEnergy(PrimitiveWithInfer):
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class Dihedral14LJForce(PrimitiveWithInfer):
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"""
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Dihedral14LJForce:
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Calculate the Lennard-Jones part of 1,4 dihedral force correction
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for each necessary dihedral terms on the corresponding atoms.
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Calculate the Lennard-Jones part of 1,4 dihedral force correction for
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each necessary dihedral terms on the corresponding atoms. Assume the
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number of necessary dihedral 1,4 terms is M, the number of atoms is N,
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Assume the number of necessary dihedral 1,4 terms is M, the number of atoms is N,
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and the number of Lennard-Jones types for all atoms is P, which means
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there will be Q = P*(P+1)/2 types of possible Lennard-Jones interactions
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for all kinds of atom pairs.
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@ -901,7 +959,7 @@ class Dihedral14LJForce(PrimitiveWithInfer):
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F = k*(-12*A/|dr|^{14} + 6*B/|dr|^{8})*dr
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Args:
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dihedral_14_numbers (int32): the number of necessary dihedral 1,4 terms M.
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nb14_numbers (int32): the number of necessary dihedral 1,4 terms M.
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atom_numbers (int32): the number of atoms N.
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Inputs:
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@ -958,8 +1016,6 @@ class Dihedral14LJForce(PrimitiveWithInfer):
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class Dihedral14LJEnergy(PrimitiveWithInfer):
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"""
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Dihedral14LJEnergy:
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Calculate the Lennard-Jones part of 1,4 dihedral energy correction for
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each necessary dihedral terms on the corresponding atoms.
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@ -969,10 +1025,20 @@ class Dihedral14LJEnergy(PrimitiveWithInfer):
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E = k*(A/|dr|^{12} - B/|dr|^{6})
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Args:
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Same as operator Dihedral14LJForce().
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nb14_numbers (int32): the number of necessary dihedral 1,4 terms M.
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atom_numbers (int32): the number of atoms N.
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Inputs:
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Same as operator Dihedral14LJForce().
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- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
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- **LJ_type** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
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- **charge** (Tensor, float32) - [N,], the charge of each atom.
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- **boxlength_f** (Tensor, float32) - [3,], the length of molecular simulation box in 3 dimensions.
|
||||
- **a_14** (Tensor, int32) - [M,], the first atom index of each dihedral 1,4 term.
|
||||
- **b_14** (Tensor, int32) - [M,], the second atom index of each dihedral 1,4 term.
|
||||
- **lj_scale_factor** (Tensor, float32) - [M,], the scale factor for the
|
||||
Lennard-Jones part of force correction of each dihedral 1,4 term.
|
||||
- **LJ_type_A** (Tensor, float32) - [Q,], the A parameter in Lennard-Jones scheme of each atom pair type.
|
||||
- **LJ_type_B** (Tensor, float32) - [Q,], the B parameter in Lennard-Jones shceme of each atom pair type.
|
||||
|
||||
Outputs:
|
||||
- **ene** (Tensor, float32) - [M,], the Lennard-Jones potential
|
||||
|
|
@ -1017,8 +1083,6 @@ class Dihedral14LJEnergy(PrimitiveWithInfer):
|
|||
|
||||
class Dihedral14LJForceWithDirectCF(PrimitiveWithInfer):
|
||||
"""
|
||||
Dihedral14LJForceWithDirectCF:
|
||||
|
||||
Calculate the Lennard-Jones part and the Coulomb part of force correction
|
||||
for each necessary dihedral 1,4 terms.
|
||||
|
||||
|
|
@ -1031,13 +1095,22 @@ class Dihedral14LJForceWithDirectCF(PrimitiveWithInfer):
|
|||
F = -k*q_a*q_b/|r|^3*dr
|
||||
|
||||
Args:
|
||||
Same as operator Dihedral14LJForce().
|
||||
nb14_numbers (int32): the number of necessary dihedral 1,4 terms M.
|
||||
atom_numbers (int32): the number of atoms N.
|
||||
|
||||
Inputs:
|
||||
- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
|
||||
- **LJ_type** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge of each atom.
|
||||
- **boxlength_f** (Tensor, float32) - [3,], the length of molecular simulation box in 3 dimensions.
|
||||
- **a_14** (Tensor, int32) - [M,], the first atom index of each dihedral 1,4 term.
|
||||
- **b_14** (Tensor, int32) - [M,], the second atom index of each dihedral 1,4 term.
|
||||
- **lj_scale_factor** (Tensor, float32) - [M,], the scale factor for the
|
||||
Lennard-Jones part of force correction of each dihedral 1,4 term.
|
||||
- **cf_scale_factor** (Tensor, float) - [M,], the scale factor for the
|
||||
Coulomb part of force correction for each dihedral 1,4 terms.
|
||||
|
||||
The rest of the inputs is the same as operator Dihedral14LJForce().
|
||||
- **LJ_type_A** (Tensor, float32) - [Q,], the A parameter in Lennard-Jones scheme of each atom pair type.
|
||||
- **LJ_type_B** (Tensor, float32) - [Q,], the B parameter in Lennard-Jones shceme of each atom pair type.
|
||||
|
||||
Outputs:
|
||||
- **frc_f** (Tensor, float) - [N, 3], the force felt by each atom.
|
||||
|
|
@ -1083,8 +1156,6 @@ class Dihedral14LJForceWithDirectCF(PrimitiveWithInfer):
|
|||
|
||||
class Dihedral14LJCFForceWithAtomEnergy(PrimitiveWithInfer):
|
||||
"""
|
||||
Dihedral14LJCFForceWithAtomEnergy:
|
||||
|
||||
Calculate the Lennard-Jones and Coulumb energy correction and force correction
|
||||
for each necessary dihedral 1,4 terms together and add them to the total force
|
||||
and potential energy for each atom.
|
||||
|
|
@ -1094,10 +1165,22 @@ class Dihedral14LJCFForceWithAtomEnergy(PrimitiveWithInfer):
|
|||
as operator Dihedral14LJEnergy() and Dihedral14CFEnergy().
|
||||
|
||||
Args:
|
||||
Same as operator Dihedral14LJForce().
|
||||
nb14_numbers (int32): the number of necessary dihedral 1,4 terms M.
|
||||
atom_numbers (int32): the number of atoms N.
|
||||
|
||||
Inputs:
|
||||
Same as operator Dihedral14LJForceWithdirectCF().
|
||||
- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
|
||||
- **LJ_type** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge of each atom.
|
||||
- **boxlength_f** (Tensor, float32) - [3,], the length of molecular simulation box in 3 dimensions.
|
||||
- **a_14** (Tensor, int32) - [M,], the first atom index of each dihedral 1,4 term.
|
||||
- **b_14** (Tensor, int32) - [M,], the second atom index of each dihedral 1,4 term.
|
||||
- **lj_scale_factor** (Tensor, float32) - [M,], the scale factor for the
|
||||
Lennard-Jones part of force correction of each dihedral 1,4 term.
|
||||
- **cf_scale_factor** (Tensor, float) - [M,], the scale factor for the
|
||||
Coulomb part of force correction for each dihedral 1,4 terms.
|
||||
- **LJ_type_A** (Tensor, float32) - [Q,], the A parameter in Lennard-Jones scheme of each atom pair type.
|
||||
- **LJ_type_B** (Tensor, float32) - [Q,], the B parameter in Lennard-Jones shceme of each atom pair type.
|
||||
|
||||
Outputs:
|
||||
- **frc_f** (Tensor, float32) - [N, 3], the force felt by each atom.
|
||||
|
|
@ -1144,18 +1227,26 @@ class Dihedral14LJCFForceWithAtomEnergy(PrimitiveWithInfer):
|
|||
|
||||
class Dihedral14LJAtomEnergy(PrimitiveWithInfer):
|
||||
"""
|
||||
Dihedral14LJAtomEnergy:
|
||||
|
||||
Add the potenrial energy caused by Lennard-Jones energy correction for each
|
||||
necessary dihedral 1,4 terms to the total potential energy of each atom.
|
||||
|
||||
The calculation formula is the same as operator Dihedral14LJEnergy().
|
||||
|
||||
Args:
|
||||
Same as operator Dihedral14LJForce().
|
||||
nb14_numbers (int32): the number of necessary dihedral 1,4 terms M.
|
||||
atom_numbers (int32): the number of atoms N.
|
||||
|
||||
Inputs:
|
||||
Same as operator Dihedral14LJForce().
|
||||
- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
|
||||
- **LJ_type** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge of each atom.
|
||||
- **boxlength_f** (Tensor, float32) - [3,], the length of molecular simulation box in 3 dimensions.
|
||||
- **a_14** (Tensor, int32) - [M,], the first atom index of each dihedral 1,4 term.
|
||||
- **b_14** (Tensor, int32) - [M,], the second atom index of each dihedral 1,4 term.
|
||||
- **lj_scale_factor** (Tensor, float32) - [M,], the scale factor for the
|
||||
Lennard-Jones part of force correction of each dihedral 1,4 term.
|
||||
- **LJ_type_A** (Tensor, float32) - [Q,], the A parameter in Lennard-Jones scheme of each atom pair type.
|
||||
- **LJ_type_B** (Tensor, float32) - [Q,], the B parameter in Lennard-Jones shceme of each atom pair type.
|
||||
|
||||
Outputs:
|
||||
- **ene** (Tensor, float32) - [N,], the accumulated potential energy of each atom.
|
||||
|
|
@ -1200,8 +1291,6 @@ class Dihedral14LJAtomEnergy(PrimitiveWithInfer):
|
|||
|
||||
class Dihedral14CFEnergy(PrimitiveWithInfer):
|
||||
"""
|
||||
Dihedral14CFEnergy:
|
||||
|
||||
Calculate the Coulumb part of 1,4 dihedral energy correction for
|
||||
each necessary dihedral terms on the corresponding atoms.
|
||||
|
||||
|
|
@ -1211,10 +1300,18 @@ class Dihedral14CFEnergy(PrimitiveWithInfer):
|
|||
E = k*q_a*q_b/|dr|
|
||||
|
||||
Args:
|
||||
Same as operator Dihedral14LJForce().
|
||||
nb14_numbers (int32): the number of necessary dihedral 1,4 terms M.
|
||||
atom_numbers (int32): the number of atoms N.
|
||||
|
||||
Inputs:
|
||||
The meaning and type of each input is the same as that of operator Dihedral14LJForceWithDirectCF().
|
||||
- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
|
||||
- **LJ_type** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge of each atom.
|
||||
- **boxlength_f** (Tensor, float32) - [3,], the length of molecular simulation box in 3 dimensions.
|
||||
- **a_14** (Tensor, int32) - [M,], the first atom index of each dihedral 1,4 term.
|
||||
- **b_14** (Tensor, int32) - [M,], the second atom index of each dihedral 1,4 term.
|
||||
- **cf_scale_factor** (Tensor, float) - [M,], the scale factor for the
|
||||
Coulomb part of force correction for each dihedral 1,4 terms.
|
||||
|
||||
Outputs:
|
||||
- **ene** (Tensor, float32) - [M,], the accumulated potential energy of each atom.
|
||||
|
|
@ -1256,18 +1353,24 @@ class Dihedral14CFEnergy(PrimitiveWithInfer):
|
|||
|
||||
class Dihedral14CFAtomEnergy(PrimitiveWithInfer):
|
||||
"""
|
||||
Dihedral14CFAtomEnergy:
|
||||
|
||||
Add the potential energy caused by Coulumb energy correction for each
|
||||
necessary dihedral 1,4 terms to the total potential energy of each atom.
|
||||
|
||||
The calculation formula is the same as operator Dihedral14CFEnergy().
|
||||
|
||||
Args:
|
||||
Same as operator Dihedral14LJForce().
|
||||
nb14_numbers (int32): the number of necessary dihedral 1,4 terms M.
|
||||
atom_numbers (int32): the number of atoms N.
|
||||
|
||||
Inputs:
|
||||
The meaning and type of each input is the same as that of operator Dihedral14LJForceWithDirectCF().
|
||||
- **uint_crd_f** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
|
||||
- **LJ_type** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge of each atom.
|
||||
- **boxlength_f** (Tensor, float32) - [3,], the length of molecular simulation box in 3 dimensions.
|
||||
- **a_14** (Tensor, int32) - [M,], the first atom index of each dihedral 1,4 term.
|
||||
- **b_14** (Tensor, int32) - [M,], the second atom index of each dihedral 1,4 term.
|
||||
- **cf_scale_factor** (Tensor, float) - [M,], the scale factor for the
|
||||
Coulomb part of force correction for each dihedral 1,4 terms.
|
||||
|
||||
Outputs:
|
||||
- **ene** (Tensor, float32) - [N,], the accumulated potential energy of each atom.
|
||||
|
|
@ -1310,8 +1413,6 @@ class Dihedral14CFAtomEnergy(PrimitiveWithInfer):
|
|||
|
||||
class MDIterationLeapFrog(PrimitiveWithInfer):
|
||||
"""
|
||||
MDIterationLeapFrog:
|
||||
|
||||
One step of classical leap frog algorithm to solve the finite difference
|
||||
Hamiltonian equations of motion for certain system, using Langevin dynamics
|
||||
with Liu's thermostat scheme. Assume the number of atoms is N and the target
|
||||
|
|
@ -1387,8 +1488,6 @@ class MDIterationLeapFrog(PrimitiveWithInfer):
|
|||
|
||||
class PMEReciprocalForce(PrimitiveWithInfer):
|
||||
"""
|
||||
PMEReciprocalForce:
|
||||
|
||||
Calculate the reciprocal part of long-range Coulumb force using
|
||||
PME(Particle Meshed Ewald) method. Assume the number of atoms is N.
|
||||
|
||||
|
|
@ -1413,7 +1512,7 @@ class PMEReciprocalForce(PrimitiveWithInfer):
|
|||
- **force** (Tensor, float32) - [N, 3], the force felt by each atom.
|
||||
|
||||
Supported Platforms:
|
||||
```GPU```
|
||||
``GPU``
|
||||
"""
|
||||
|
||||
@prim_attr_register
|
||||
|
|
@ -1448,8 +1547,6 @@ class PMEReciprocalForce(PrimitiveWithInfer):
|
|||
|
||||
class PMEExcludedForce(PrimitiveWithInfer):
|
||||
"""
|
||||
PMEExcludedForce:
|
||||
|
||||
Calculate the excluded part of long-range Coulumb force using
|
||||
PME(Particle Meshed Ewald) method. Assume the number of atoms is
|
||||
N, and the length of excluded list is E.
|
||||
|
|
@ -1460,22 +1557,22 @@ class PMEExcludedForce(PrimitiveWithInfer):
|
|||
non-bond cutoff value and simulation precision tolerance.
|
||||
|
||||
Inputs:
|
||||
- **uint_crd** (Tensor, uint32) - [N, 3], the unsigned int coordinates value of each atom.
|
||||
- **scaler** (Tensor, float32) - [3,], the scale factor between real space
|
||||
coordinates and its unsigned int value.
|
||||
- **charge** (Tensor, float32) - [N,], the charge carried by each atom.
|
||||
- **excluded_list_start** (Tensor, int32) - [N,], the start excluded index
|
||||
in excluded list for each atom.
|
||||
- **excluded_numbers** (Tensor, int32) - [N,], the number of atom excluded
|
||||
in excluded list for each atom.
|
||||
- **excluded_list** (Tensor, int32) - [E,], the contiguous join of excluded
|
||||
list of each atom.
|
||||
|
||||
The rest of the input is the same as that of operator PMEReciprocalForce().
|
||||
- **excluded_atom_numbers** (Tensor, int32) - [N,], the number of atom excluded
|
||||
in excluded list for each atom.
|
||||
|
||||
Outputs:
|
||||
- **force** (Tensor, float32) - [N, 3], the force felt by each atom.
|
||||
|
||||
Supported Platforms:
|
||||
```GPU```
|
||||
``GPU``
|
||||
"""
|
||||
|
||||
@prim_attr_register
|
||||
|
|
@ -1510,8 +1607,6 @@ class PMEExcludedForce(PrimitiveWithInfer):
|
|||
|
||||
class PMEEnergy(PrimitiveWithInfer):
|
||||
"""
|
||||
PMEEnergy:
|
||||
|
||||
Calculate the Coulumb energy of the system using PME method.
|
||||
|
||||
.. math::
|
||||
|
|
@ -1519,11 +1614,27 @@ class PMEEnergy(PrimitiveWithInfer):
|
|||
E = sum_{ij} q_iq_j/r_{ij}
|
||||
|
||||
Args:
|
||||
same as operator PMEReciprocalForce().
|
||||
atom_numbers(int32): the number of atoms, N.
|
||||
beta(float32): the PME beta parameter, determined by the
|
||||
non-bond cutoff value and simulation precision tolerance.
|
||||
fftx(int32): the number of points for Fourier transform in dimension X.
|
||||
ffty(int32): the number of points for Fourier transform in dimension Y.
|
||||
fftz(int32): the number of points for Fourier transform in dimension Z.
|
||||
|
||||
Inputs:
|
||||
Same as operator PMEReciprocalForce(), PMEExcludedForce()
|
||||
and PMEDirectAtomEnergy().
|
||||
- **boxlength** (Tensor, float32) - [3,], the length of simulation box in 3 dimensions.
|
||||
- **uint_crd** (Tensor, uint32) - [N, 3], the unsigned int coordinates value of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge carried by each atom.
|
||||
- **nl_numbers** - (Tensor, int32) - [N,], the each atom.
|
||||
- **nl_serial** - (Tensor, int32) - [N, 800], the neighbor list of each atom, the max number is 800.
|
||||
- **scaler** (Tensor, float32) - [3,], the scale factor between real space
|
||||
coordinates and its unsigned int value.
|
||||
- **excluded_list_start** (Tensor, int32) - [N,], the start excluded index
|
||||
in excluded list for each atom.
|
||||
- **excluded_list** (Tensor, int32) - [E,], the contiguous join of excluded
|
||||
list of each atom.
|
||||
- **excluded_atom_numbers** (Tensor, int32) - [N,], the number of atom excluded
|
||||
in excluded list for each atom.
|
||||
|
||||
Outputs:
|
||||
- **reciprocal_ene** (float32) - the reciprocal term of PME energy.
|
||||
|
|
@ -1532,7 +1643,7 @@ class PMEEnergy(PrimitiveWithInfer):
|
|||
- **correction_ene** (float32) - the correction term of PME energy.
|
||||
|
||||
Supported Platforms:
|
||||
```GPU``
|
||||
``GPU``
|
||||
"""
|
||||
|
||||
@prim_attr_register
|
||||
|
|
@ -1580,8 +1691,6 @@ class PMEEnergy(PrimitiveWithInfer):
|
|||
|
||||
class LJEnergy(PrimitiveWithInfer):
|
||||
"""
|
||||
LJEnergy:
|
||||
|
||||
Calculate the Van der Waals interaction energy described by Lennard-Jones
|
||||
potential for each atom. Assume the number of atoms is N, and the number
|
||||
of Lennard-Jones types for all atoms is P, which means there will be
|
||||
|
|
@ -1614,7 +1723,7 @@ class LJEnergy(PrimitiveWithInfer):
|
|||
- **d_LJ_energy_sum** (float32), the sum of Lennard-Jones potential energy of each atom.
|
||||
|
||||
Supported Platforms:
|
||||
```GPU```
|
||||
``GPU``
|
||||
"""
|
||||
|
||||
@prim_attr_register
|
||||
|
|
@ -1646,8 +1755,6 @@ class LJEnergy(PrimitiveWithInfer):
|
|||
|
||||
class LJForce(PrimitiveWithInfer):
|
||||
"""
|
||||
LJForce:
|
||||
|
||||
Calculate the Van der Waals interaction force described by Lennard-Jones
|
||||
potential energy for each atom.
|
||||
|
||||
|
|
@ -1656,17 +1763,26 @@ class LJForce(PrimitiveWithInfer):
|
|||
dr = (x_a-x_b, y_a-y_b, z_a-z_b)
|
||||
F = (-12*A/|dr|^{14} + 6*B/|dr|^{8}) * dr
|
||||
|
||||
Args:
|
||||
Same as operator LJEnergy().
|
||||
Agrs:
|
||||
atom_numbers(int32): the number of atoms, N.
|
||||
cutoff_square(float32): the square value of cutoff.
|
||||
|
||||
Inputs:
|
||||
Same as operator LJEnergy().
|
||||
- **uint_crd** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
|
||||
- **LJtype** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge carried by each atom.
|
||||
- **scaler** (Tensor, float32) - [3,], the scale factor between real
|
||||
space coordinate and its unsigned int value.
|
||||
- **nl_numbers** - (Tensor, int32) - [N,], the each atom.
|
||||
- **nl_serial** - (Tensor, int32) - [N, 800], the neighbor list of each atom, the max number is 800.
|
||||
- **d_LJ_A** (Tensor, float32) - [Q,], the Lennard-Jones A coefficient of each kind of atom pair.
|
||||
- **d_LJ_B** (Tensor, float32) - [Q,], the Lennard-Jones B coefficient of each kind of atom pair.
|
||||
|
||||
outputs:
|
||||
- **frc** (Tensor, float32) - [N, 3], the force felt by each atom.
|
||||
|
||||
Supported Platforms:
|
||||
```GPU```
|
||||
``GPU``
|
||||
"""
|
||||
|
||||
@prim_attr_register
|
||||
|
|
@ -1698,25 +1814,32 @@ class LJForce(PrimitiveWithInfer):
|
|||
|
||||
class LJForceWithPMEDirectForce(PrimitiveWithInfer):
|
||||
"""
|
||||
LJForceWithPMEDirectForce:
|
||||
|
||||
Calculate the Lennard-Jones force and PME direct force together.
|
||||
|
||||
The calculation formula of Lennard-Jones part is the same as operator
|
||||
LJForce(), and the PME direct part is within PME method.
|
||||
|
||||
Args:
|
||||
Agrs:
|
||||
atom_numbers(int32): the number of atoms, N.
|
||||
cutoff_square(float32): the square value of cutoff.
|
||||
pme_beta(float32): PME beta parameter, same as operator PMEReciprocalForce().
|
||||
The rest is same as operator LJEnergy().
|
||||
|
||||
Inputs:
|
||||
same as operator LJForce().
|
||||
- **uint_crd** (Tensor, uint32) - [N, 3], the unsigned int coordinate value of each atom.
|
||||
- **LJtype** (Tensor, int32) - [N,], the Lennard-Jones type of each atom.
|
||||
- **charge** (Tensor, float32) - [N,], the charge carried by each atom.
|
||||
- **scaler** (Tensor, float32) - [3,], the scale factor between real
|
||||
space coordinate and its unsigned int value.
|
||||
- **nl_numbers** - (Tensor, int32) - [N,], the each atom.
|
||||
- **nl_serial** - (Tensor, int32) - [N, 800], the neighbor list of each atom, the max number is 800.
|
||||
- **d_LJ_A** (Tensor, float32) - [Q,], the Lennard-Jones A coefficient of each kind of atom pair.
|
||||
- **d_LJ_B** (Tensor, float32) - [Q,], the Lennard-Jones B coefficient of each kind of atom pair.
|
||||
|
||||
Outputs:
|
||||
- **frc** (Tensor, float32), [N, 3], the force felt by each atom.
|
||||
|
||||
Supported Platforms:
|
||||
```GPU```
|
||||
``GPU``
|
||||
"""
|
||||
|
||||
@prim_attr_register
|
||||
|
|
@ -1751,7 +1874,7 @@ class LJForceWithPMEDirectForce(PrimitiveWithInfer):
|
|||
|
||||
class GetCenterOfGeometry(PrimitiveWithInfer):
|
||||
"""
|
||||
GetCenterOfGeometry:
|
||||
Get Center Of Geometry.
|
||||
|
||||
Supported Platforms:
|
||||
``GPU``
|
||||
|
|
@ -1784,7 +1907,7 @@ class GetCenterOfGeometry(PrimitiveWithInfer):
|
|||
|
||||
class MDTemperature(PrimitiveWithInfer):
|
||||
"""
|
||||
MDTemperature:
|
||||
Calculate the MD Temperature.
|
||||
|
||||
Calculate the temperature.
|
||||
|
||||
|
|
@ -1828,8 +1951,6 @@ class MDTemperature(PrimitiveWithInfer):
|
|||
|
||||
class NeighborListUpdate(PrimitiveWithInfer):
|
||||
"""
|
||||
NeighborListUpdate
|
||||
|
||||
Update (or construct if first time) the Verlet neighbor list for the
|
||||
calculation of short-ranged force. Assume the number of atoms is N,
|
||||
the number of grids divided is G, the maximum number of atoms in one
|
||||
|
|
@ -1882,7 +2003,7 @@ class NeighborListUpdate(PrimitiveWithInfer):
|
|||
- **res** (float32)
|
||||
|
||||
Supported Platforms:
|
||||
```GPU```
|
||||
``GPU``
|
||||
"""
|
||||
|
||||
@prim_attr_register
|
||||
|
|
@ -2019,8 +2140,6 @@ class NeighborListUpdate(PrimitiveWithInfer):
|
|||
|
||||
class MDIterationLeapFrogWithRF(PrimitiveWithInfer):
|
||||
"""
|
||||
MDIterationLeapFrog:
|
||||
|
||||
One step of classical leap frog algorithm to solve the finite difference
|
||||
Hamiltonian equations of motion for certain system, using Langevin dynamics
|
||||
with Liu's thermostat scheme. Assume the number of atoms is N and the target
|
||||
|
|
|
|||
Loading…
Reference in New Issue