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lmp: support unit real #2775

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Sep 2, 2023
Merged

lmp: support unit real #2775

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3005664
lmp: support unit real
njzjz Jul 13, 2023
5162233
fix typo
njzjz Jul 13, 2023
b1f131a
Update test_lammps.py
njzjz Jul 13, 2023
a9bb26b
fix scale
njzjz Jul 13, 2023
514bead
Merge branch 'devel' into lmp-different-unit
njzjz Aug 31, 2023
2befd23
merge; fix timestep
njzjz Aug 31, 2023
4d78282
do not declare
njzjz Aug 31, 2023
b2828da
== -> =
njzjz Sep 1, 2023
faf8d4b
fix typo
njzjz Sep 1, 2023
eff7679
fix typo
njzjz Sep 1, 2023
bf4c692
nktv2p_real
njzjz Sep 1, 2023
dd078e3
keep scale; rename conversion_factor
njzjz Sep 1, 2023
dba21a3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 1, 2023
a7b8b87
update the header file
njzjz Sep 1, 2023
40e4c86
convert model deviation
njzjz Sep 1, 2023
8a4222e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 1, 2023
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80 changes: 45 additions & 35 deletions source/lmp/pair_deepmd.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -344,11 +344,17 @@ PairDeepMD::PairDeepMD(LAMMPS *lmp)
if (lmp->citeme) {
lmp->citeme->add(cite_user_deepmd_package);
}
if (strcmp(update->unit_style, "metal") != 0) {
error->all(
FLERR,
"Pair deepmd requires metal unit, please set it by \"units metal\"");
int unit_convert;
if (strcmp(update->unit_style, "metal") == 0) {
unit_convert = utils::NOCONVERT;
} else if (strcmp(update->unit_style, "real") == 0) {
unit_convert = utils::METAL2REAL;
} else {
error->all(FLERR,
"Pair deepmd requires metal or real unit, please set it by "
"\"units metal\" or \"units real\"");
}
conversion_factor = utils::get_conversion_factor(utils::ENERGY, unit_convert);
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restartinfo = 1;
#if LAMMPS_VERSION_NUMBER >= 20201130
centroidstressflag =
Expand All @@ -361,6 +367,8 @@ PairDeepMD::PairDeepMD(LAMMPS *lmp)
pppmflag = 1;
respa_enable = 0;
writedata = 0;
unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);

cutoff = 0.;
numb_types = 0;
numb_types_spin = 0;
Expand Down Expand Up @@ -576,7 +584,7 @@ void PairDeepMD::compute(int eflag, int vflag) {
}
if (eflag_atom) {
for (int ii = 0; ii < nlocal; ++ii) {
eatom[ii] += deatom[ii];
eatom[ii] += conversion_factor * deatom[ii];
}
}
// Added by Davide Tisi 2020
Expand All @@ -590,15 +598,15 @@ void PairDeepMD::compute(int eflag, int vflag) {
// vatom[ii][3] += 1.0 * dvatom[9*ii+3];
// vatom[ii][4] += 1.0 * dvatom[9*ii+6];
// vatom[ii][5] += 1.0 * dvatom[9*ii+7];
cvatom[ii][0] += 1.0 * dvatom[9 * ii + 0]; // xx
cvatom[ii][1] += 1.0 * dvatom[9 * ii + 4]; // yy
cvatom[ii][2] += 1.0 * dvatom[9 * ii + 8]; // zz
cvatom[ii][3] += 1.0 * dvatom[9 * ii + 3]; // xy
cvatom[ii][4] += 1.0 * dvatom[9 * ii + 6]; // xz
cvatom[ii][5] += 1.0 * dvatom[9 * ii + 7]; // yz
cvatom[ii][6] += 1.0 * dvatom[9 * ii + 1]; // yx
cvatom[ii][7] += 1.0 * dvatom[9 * ii + 2]; // zx
cvatom[ii][8] += 1.0 * dvatom[9 * ii + 5]; // zy
cvatom[ii][0] += conversion_factor * dvatom[9 * ii + 0]; // xx
cvatom[ii][1] += conversion_factor * dvatom[9 * ii + 4]; // yy
cvatom[ii][2] += conversion_factor * dvatom[9 * ii + 8]; // zz
cvatom[ii][3] += conversion_factor * dvatom[9 * ii + 3]; // xy
cvatom[ii][4] += conversion_factor * dvatom[9 * ii + 6]; // xz
cvatom[ii][5] += conversion_factor * dvatom[9 * ii + 7]; // yz
cvatom[ii][6] += conversion_factor * dvatom[9 * ii + 1]; // yx
cvatom[ii][7] += conversion_factor * dvatom[9 * ii + 2]; // zx
cvatom[ii][8] += conversion_factor * dvatom[9 * ii + 5]; // zy
}
}
}
Expand Down Expand Up @@ -628,7 +636,7 @@ void PairDeepMD::compute(int eflag, int vflag) {
dvatom = all_atom_virial[0];
if (eflag_atom) {
for (int ii = 0; ii < nlocal; ++ii) {
eatom[ii] += deatom[ii];
eatom[ii] += conversion_factor * deatom[ii];
}
}
// Added by Davide Tisi 2020
Expand All @@ -642,15 +650,15 @@ void PairDeepMD::compute(int eflag, int vflag) {
// vatom[ii][3] += 1.0 * dvatom[9*ii+3];
// vatom[ii][4] += 1.0 * dvatom[9*ii+6];
// vatom[ii][5] += 1.0 * dvatom[9*ii+7];
cvatom[ii][0] += 1.0 * dvatom[9 * ii + 0]; // xx
cvatom[ii][1] += 1.0 * dvatom[9 * ii + 4]; // yy
cvatom[ii][2] += 1.0 * dvatom[9 * ii + 8]; // zz
cvatom[ii][3] += 1.0 * dvatom[9 * ii + 3]; // xy
cvatom[ii][4] += 1.0 * dvatom[9 * ii + 6]; // xz
cvatom[ii][5] += 1.0 * dvatom[9 * ii + 7]; // yz
cvatom[ii][6] += 1.0 * dvatom[9 * ii + 1]; // yx
cvatom[ii][7] += 1.0 * dvatom[9 * ii + 2]; // zx
cvatom[ii][8] += 1.0 * dvatom[9 * ii + 5]; // zy
cvatom[ii][0] += conversion_factor * dvatom[9 * ii + 0]; // xx
cvatom[ii][1] += conversion_factor * dvatom[9 * ii + 4]; // yy
cvatom[ii][2] += conversion_factor * dvatom[9 * ii + 8]; // zz
cvatom[ii][3] += conversion_factor * dvatom[9 * ii + 3]; // xy
cvatom[ii][4] += conversion_factor * dvatom[9 * ii + 6]; // xz
cvatom[ii][5] += conversion_factor * dvatom[9 * ii + 7]; // yz
cvatom[ii][6] += conversion_factor * dvatom[9 * ii + 1]; // yx
cvatom[ii][7] += conversion_factor * dvatom[9 * ii + 2]; // zx
cvatom[ii][8] += conversion_factor * dvatom[9 * ii + 5]; // zy
}
}
if (out_freq > 0 && update->ntimestep % out_freq == 0) {
Expand Down Expand Up @@ -774,7 +782,7 @@ void PairDeepMD::compute(int eflag, int vflag) {
if (!atom->sp_flag) {
for (int ii = 0; ii < nall; ++ii) {
for (int dd = 0; dd < 3; ++dd) {
f[ii][dd] += scale[1][1] * dforce[3 * ii + dd];
f[ii][dd] += conversion_factor * dforce[3 * ii + dd];
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}
}
} else {
Expand All @@ -783,12 +791,14 @@ void PairDeepMD::compute(int eflag, int vflag) {
for (int ii = 0; ii < nall; ++ii) {
for (int dd = 0; dd < 3; ++dd) {
int new_idx = new_idx_map[ii];
f[ii][dd] += scale[1][1] * dforce[3 * new_idx + dd];
f[ii][dd] += conversion_factor * dforce[3 * new_idx + dd];
if (dtype[ii] < numb_types_spin && ii < nlocal) {
fm[ii][dd] += scale[1][1] * dforce[3 * (new_idx + nlocal) + dd] /
fm[ii][dd] += conversion_factor *
dforce[3 * (new_idx + nlocal) + dd] /
(hbar / spin_norm[dtype[ii]]);
} else if (dtype[ii] < numb_types_spin) {
fm[ii][dd] += scale[1][1] * dforce[3 * (new_idx + nghost) + dd] /
fm[ii][dd] += conversion_factor *
dforce[3 * (new_idx + nghost) + dd] /
(hbar / spin_norm[dtype[ii]]);
}
}
Expand All @@ -803,15 +813,15 @@ void PairDeepMD::compute(int eflag, int vflag) {

// accumulate energy and virial
if (eflag) {
eng_vdwl += scale[1][1] * dener;
eng_vdwl += conversion_factor * dener;
}
if (vflag) {
virial[0] += 1.0 * dvirial[0] * scale[1][1];
virial[1] += 1.0 * dvirial[4] * scale[1][1];
virial[2] += 1.0 * dvirial[8] * scale[1][1];
virial[3] += 1.0 * dvirial[3] * scale[1][1];
virial[4] += 1.0 * dvirial[6] * scale[1][1];
virial[5] += 1.0 * dvirial[7] * scale[1][1];
virial[0] += 1.0 * dvirial[0] * conversion_factor;
virial[1] += 1.0 * dvirial[4] * conversion_factor;
virial[2] += 1.0 * dvirial[8] * conversion_factor;
virial[3] += 1.0 * dvirial[3] * conversion_factor;
virial[4] += 1.0 * dvirial[6] * conversion_factor;
virial[5] += 1.0 * dvirial[7] * conversion_factor;
}
}

Expand Down
1 change: 1 addition & 0 deletions source/lmp/pair_deepmd.h
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,7 @@ class PairDeepMD : public Pair {
tagint *tagsend, *tagrecv;
double *stdfsend, *stdfrecv;
std::vector<int> type_idx_map;
double conversion_factor;
};

} // namespace LAMMPS_NS
Expand Down
55 changes: 52 additions & 3 deletions source/lmp/tests/test_lammps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -217,6 +217,8 @@

# https://github.com/lammps/lammps/blob/1e1311cf401c5fc2614b5d6d0ff3230642b76597/src/update.cpp#L193
nktv2p = 1.6021765e6
nktv2p_real = 68568.415
metal2real = 23.060549

sp.check_output(
"{} -m deepmd convert-from pbtxt -i {} -o {}".format(
Expand Down Expand Up @@ -244,17 +246,22 @@ def teardown_module():
os.remove(data_type_map_file)


def _lammps(data_file) -> PyLammps:
def _lammps(data_file, units="metal") -> PyLammps:
lammps = PyLammps()
lammps.units("metal")
lammps.units(units)
lammps.boundary("p p p")
lammps.atom_style("atomic")
lammps.neighbor("2.0 bin")
lammps.neigh_modify("every 10 delay 0 check no")
lammps.read_data(data_file.resolve())
lammps.mass("1 16")
lammps.mass("2 2")
lammps.timestep(0.0005)
if units == "metal":
lammps.timestep(0.0005)
elif units == "real":
lammps.timestep(0.5)
else:
raise ValueError("units should be metal or real")
lammps.fix("1 all nve")
return lammps

Expand All @@ -273,6 +280,13 @@ def lammps_type_map():
lmp.close()


@pytest.fixture
def lammps_real():
lmp = _lammps(data_file=data_file, units="real")
yield lmp
lmp.close()


def test_pair_deepmd(lammps):
lammps.pair_style(f"deepmd {pb_file.resolve()}")
lammps.pair_coeff("* *")
Expand Down Expand Up @@ -452,3 +466,38 @@ def test_pair_deepmd_type_map(lammps_type_map):
expected_f[lammps_type_map.atoms[ii].id - 1]
)
lammps_type_map.run(1)


def test_pair_deepmd_real(lammps_real):
lammps_real.pair_style(f"deepmd {pb_file.resolve()}")
lammps_real.pair_coeff("* *")
lammps_real.run(0)
assert lammps_real.eval("pe") == pytest.approx(expected_e * metal2real)
for ii in range(6):
assert lammps_real.atoms[ii].force == pytest.approx(
expected_f[lammps_real.atoms[ii].id - 1] * metal2real
)
lammps_real.run(1)


def test_pair_deepmd_virial_real(lammps_real):
lammps_real.pair_style(f"deepmd {pb_file.resolve()}")
lammps_real.pair_coeff("* *")
lammps_real.compute("virial all centroid/stress/atom NULL pair")
for ii in range(9):
jj = [0, 4, 8, 3, 6, 7, 1, 2, 5][ii]
lammps_real.variable(f"virial{jj} atom c_virial[{ii+1}]")
lammps_real.dump(
"1 all custom 1 dump id " + " ".join([f"v_virial{ii}" for ii in range(9)])
)
lammps_real.run(0)
assert lammps_real.eval("pe") == pytest.approx(expected_e * metal2real)
for ii in range(6):
assert lammps_real.atoms[ii].force == pytest.approx(
expected_f[lammps_real.atoms[ii].id - 1] * metal2real
)
idx_map = lammps_real.lmp.numpy.extract_atom("id") - 1
for ii in range(9):
assert np.array(
lammps_real.variables[f"virial{ii}"].value
) / nktv2p_real == pytest.approx(expected_v[idx_map, ii] * metal2real)