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Merged
wanghan-iapcm merged 11 commits into from
Jun 5, 2023
Merged

Support minimization in dplr #2584

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8f688a9
support minimization in dplr
Yi-FanLi Jun 2, 2023
d8243c9
check if the periodic images of a bonded pair are on the same processor
Yi-FanLi Jun 2, 2023
74d2b58
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 2, 2023
4eb8fbb
fix a bug in get_valid_pairs
Yi-FanLi Jun 3, 2023
96fa9d4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 3, 2023
752006b
The correct local atom index range is >= 0.
Yi-FanLi Jun 3, 2023
4818fbf
revert the changes in get_valid_pairs
Yi-FanLi Jun 3, 2023
cce82dd
Use min_pre_exchange to make WC positioned at corresponding real atom…
Yi-FanLi Jun 3, 2023
545448c
Declare min_pre_exchange in fix_dplr.h
Yi-FanLi Jun 3, 2023
c303b00
add unittest for minimize dplr
Yi-FanLi Jun 3, 2023
85359a1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 3, 2023
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37 changes: 37 additions & 0 deletions source/lmp/fix_dplr.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -125,6 +125,8 @@ FixDPLR::FixDPLR(LAMMPS *lmp, int narg, char **arg)
comm_reverse = 3;
}

/* ---------------------------------------------------------------------- */

int FixDPLR::setmask() {
int mask = 0;
#if LAMMPS_VERSION_NUMBER < 20210210
Expand All @@ -134,9 +136,14 @@ int FixDPLR::setmask() {
mask |= POST_INTEGRATE;
mask |= PRE_FORCE;
mask |= POST_FORCE;
mask |= MIN_PRE_EXCHANGE;
mask |= MIN_PRE_FORCE;
mask |= MIN_POST_FORCE;
return mask;
}

/* ---------------------------------------------------------------------- */

void FixDPLR::init() {
// double **xx = atom->x;
// double **vv = atom->v;
Expand All @@ -152,8 +159,12 @@ void FixDPLR::init() {
// }
}

/* ---------------------------------------------------------------------- */

void FixDPLR::setup_pre_force(int vflag) { pre_force(vflag); }

/* ---------------------------------------------------------------------- */

void FixDPLR::setup(int vflag) {
// if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
Expand All @@ -167,6 +178,12 @@ void FixDPLR::setup(int vflag) {
}
}

/* ---------------------------------------------------------------------- */

void FixDPLR::min_setup(int vflag) { setup(vflag); }

/* ---------------------------------------------------------------------- */

void FixDPLR::get_valid_pairs(vector<pair<int, int> > &pairs) {
pairs.clear();

Expand Down Expand Up @@ -215,6 +232,8 @@ void FixDPLR::get_valid_pairs(vector<pair<int, int> > &pairs) {
}
}

/* ---------------------------------------------------------------------- */

void FixDPLR::post_integrate() {
double **x = atom->x;
double **v = atom->v;
Expand All @@ -237,6 +256,8 @@ void FixDPLR::post_integrate() {
}
}

/* ---------------------------------------------------------------------- */

void FixDPLR::pre_force(int vflag) {
double **x = atom->x;
int *type = atom->type;
Expand Down Expand Up @@ -356,6 +377,8 @@ void FixDPLR::pre_force(int vflag) {
// }
}

/* ---------------------------------------------------------------------- */

void FixDPLR::post_force(int vflag) {
if (vflag) {
v_setup(vflag);
Expand Down Expand Up @@ -515,6 +538,20 @@ void FixDPLR::post_force(int vflag) {
}
}

/* ---------------------------------------------------------------------- */

void FixDPLR::min_pre_exchange() { post_integrate(); }

/* ---------------------------------------------------------------------- */

void FixDPLR::min_pre_force(int vflag) { pre_force(vflag); }

/* ---------------------------------------------------------------------- */

void FixDPLR::min_post_force(int vflag) { post_force(vflag); }

/* ---------------------------------------------------------------------- */

int FixDPLR::pack_reverse_comm(int n, int first, double *buf) {
int m = 0;
int last = first + n;
Expand Down
6 changes: 5 additions & 1 deletion source/lmp/fix_dplr.h
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Original file line number Diff line number Diff line change
Expand Up @@ -40,11 +40,15 @@ class FixDPLR : public Fix {
~FixDPLR() override{};
int setmask() override;
void init() override;
void setup_pre_force(int) override;
void setup(int) override;
void setup_pre_force(int) override;
void min_setup(int) override;
void post_integrate() override;
void pre_force(int) override;
void post_force(int) override;
void min_pre_exchange() override;
void min_pre_force(int) override;
void min_post_force(int) override;
int pack_reverse_comm(int, int, double *) override;
void unpack_reverse_comm(int, int *, double *) override;
double compute_scalar(void) override;
Expand Down
56 changes: 53 additions & 3 deletions source/lmp/tests/test_dplr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -126,6 +126,36 @@
]
)

expected_x_min_step1 = np.array(
[
[1.26321372, 1.28623039, 0.97992808],
[0.94931355, 3.25164736, 1.32847644],
[0.64743204, 1.32472127, 1.76763885],
[1.30026330, 0.31505758, 0.71705476],
[1.91176075, 3.50957943, 1.43047464],
[0.50553664, 4.04638297, 0.90796723],
[1.22952996, 1.15353755, 1.01171484],
[0.97744342, 3.38790804, 1.31885315],
]
)

expected_e_min_step1 = -40.46708779

expected_e_kspace_min_step1 = 0.16209504

expected_f_min_step1 = np.array(
[
[-0.04230911, -0.09057170, -0.00644688],
[0.03377777, 0.01767955, -0.18004346],
[-0.10280108, 0.22936656, 0.17841170],
[0.13239183, 0.02472290, -0.12924794],
[0.11956397, -0.13352759, 0.08242015],
[-0.14062339, -0.04766971, 0.05490644],
[0.00000000, 0.00000000, 0.00000000],
[0.00000000, 0.00000000, 0.00000000],
]
)

box = np.array([0, 20, 0, 20, 0, 20, 0, 0, 0])
coord = np.array(
[
Expand Down Expand Up @@ -230,10 +260,30 @@ def test_pair_deepmd_lr(lammps):
lammps.fix(f"0 all dplr model {pb_file.resolve()} type_associate 1 3 bond_type 1")
lammps.fix_modify("0 virial yes")
lammps.run(0)
assert lammps.eval("pe") == pytest.approx(expected_e_lr)
for ii in range(2):
assert lammps.atoms[6 + ii].position == pytest.approx(expected_WC[ii])
assert lammps.eval("elong") == pytest.approx(expected_e_kspace)
assert lammps.eval("pe") == pytest.approx(expected_e_lr)
for ii in range(6):
assert lammps.atoms[ii].force == pytest.approx(expected_f_lr[ii])
for ii in range(2):
assert lammps.atoms[6 + ii].position == pytest.approx(expected_WC[ii])
lammps.run(1)


def test_min_dplr(lammps):
lammps.pair_style(f"deepmd {pb_file.resolve()}")
lammps.pair_coeff("* *")
lammps.bond_style("zero")
lammps.bond_coeff("*")
lammps.special_bonds("lj/coul 1 1 1 angle no")
lammps.kspace_style("pppm/dplr 1e-5")
lammps.kspace_modify(f"gewald {beta:.2f} diff ik mesh {mesh:d} {mesh:d} {mesh:d}")
lammps.fix(f"0 all dplr model {pb_file.resolve()} type_associate 1 3 bond_type 1")
lammps.fix_modify("0 virial yes")
lammps.min_style("cg")
lammps.minimize("0 1.0e-6 2 2")
for ii in range(8):
assert lammps.atoms[ii].position == pytest.approx(expected_x_min_step1[ii])
assert lammps.eval("pe") == pytest.approx(expected_e_min_step1)
assert lammps.eval("elong") == pytest.approx(expected_e_kspace_min_step1)
for ii in range(8):
assert lammps.atoms[ii].force == pytest.approx(expected_f_min_step1[ii])