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Merged
Yi-FanLi merged 12 commits into from
Mar 10, 2025
Merged

parse multiple epsilon values for lj/cut/soft #88

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53e8961
parse multiple epsilon values for lj/cut/soft
Yi-FanLi Mar 9, 2025
e12bc0f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 9, 2025
ddd6732
correct pair_coeff for hybrid style
Yi-FanLi Mar 9, 2025
3d47f7e
fix merge conflict
Yi-FanLi Mar 9, 2025
5a19c77
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 9, 2025
4c47b34
support multiple activation values
Yi-FanLi Mar 10, 2025
44c6d77
fix merge conflict
Yi-FanLi Mar 10, 2025
ec3544d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 10, 2025
1532b71
support using a single sigma to set sigma for all pairs
Yi-FanLi Mar 10, 2025
d197d98
Merge branch 'hti_epsilon_pair' of github.com:Yi-FanLi/dpti into hti_…
Yi-FanLi Mar 10, 2025
834a1f2
add an example for hti_liq of 2 atomic types
Yi-FanLi Mar 10, 2025
6d1259f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 10, 2025
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104 changes: 48 additions & 56 deletions dpti/hti_liq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,45 +28,64 @@ def make_iter_name(iter_index):
return "task_hti." + ("%04d" % iter_index)


def parse_lj_sigma_epsilon(ret, sparam, hybrid=False):
element_num = sparam.get("element_num", 1)
sigma_key_index = filter(
lambda t: t[0] <= t[1],
((i, j) for i in range(element_num) for j in range(element_num)),
)
activation = sparam["activation"]
epsilon = sparam.get("epsilon", None)
epsilon_0_0 = sparam.get("epsilon_0_0", None)
if hybrid:
pair_coeff_str = "lj/cut/soft "
else:
pair_coeff_str = ""
if epsilon is not None:
assert (
epsilon_0_0 is None
), "epsilon and epsilon_0_0 cannot be set at the same time"
ret += f"variable EPSILON equal {epsilon:f}\n"
for i, j in sigma_key_index:
ret += "pair_coeff {} {} {p:s}${{EPSILON}} {:f} {:f}\n".format(
i + 1,
j + 1,
pair_coeff_str,
sparam["sigma_" + str(i) + "_" + str(j)],
)
else:
assert epsilon_0_0 is not None, "epsilon or epsilon_0_0 must be set"
for i, j in sigma_key_index:
ret += "pair_coeff {} {} {:s}{:f} {:f} {:f}\n".format(
i + 1,
j + 1,
pair_coeff_str,
sparam["epsilon_" + str(i) + "_" + str(j)],
sparam["sigma_" + str(i) + "_" + str(j)],
activation,
)
return ret
Comment on lines +31 to +88
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@coderabbitai coderabbitai bot Mar 9, 2025

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⚠️ Potential issue

The new function centralizes parameter processing nicely, but contains a formatting bug.

This new function appropriately centralizes the logic for processing Lennard-Jones parameters, making the code more maintainable. However, there's a formatting error in the string template.

In line 50, the string contains a {p:s} placeholder, but no corresponding p value is provided in the .format() call. Fix it like this:

-            ret += "pair_coeff      {} {} {p:s}${{EPSILON}} {:f} {:f}\n".format(
+            ret += "pair_coeff      {} {} {}${{EPSILON}} {:f} {:f}\n".format(
                 i + 1,
                 j + 1,
                 pair_coeff_str,
                 sparam["sigma_" + str(i) + "_" + str(j)],
+                activation,
             )
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
def parse_lj_sigma_epsilon(ret, sparam, hybrid=False):
element_num = sparam.get("element_num", 1)
sigma_key_index = filter(
lambda t: t[0] <= t[1],
((i, j) for i in range(element_num) for j in range(element_num)),
)
activation = sparam["activation"]
epsilon = sparam.get("epsilon", None)
epsilon_0_0 = sparam.get("epsilon_0_0", None)
if hybrid:
pair_coeff_str = "lj/cut/soft "
else:
pair_coeff_str = ""
if epsilon is not None:
assert (
epsilon_0_0 is None
), "epsilon and epsilon_0_0 cannot be set at the same time"
ret += f"variable EPSILON equal {epsilon:f}\n"
for i, j in sigma_key_index:
ret += "pair_coeff {} {} {p:s}${{EPSILON}} {:f} {:f}\n".format(
i + 1,
j + 1,
pair_coeff_str,
sparam["sigma_" + str(i) + "_" + str(j)],
)
else:
assert epsilon_0_0 is not None, "epsilon or epsilon_0_0 must be set"
for i, j in sigma_key_index:
ret += "pair_coeff {} {} {:s}{:f} {:f} {:f}\n".format(
i + 1,
j + 1,
pair_coeff_str,
sparam["epsilon_" + str(i) + "_" + str(j)],
sparam["sigma_" + str(i) + "_" + str(j)],
activation,
)
return ret
def parse_lj_sigma_epsilon(ret, sparam, hybrid=False):
element_num = sparam.get("element_num", 1)
sigma_key_index = filter(
lambda t: t[0] <= t[1],
((i, j) for i in range(element_num) for j in range(element_num)),
)
activation = sparam["activation"]
epsilon = sparam.get("epsilon", None)
epsilon_0_0 = sparam.get("epsilon_0_0", None)
if hybrid:
pair_coeff_str = "lj/cut/soft "
else:
pair_coeff_str = ""
if epsilon is not None:
assert (
epsilon_0_0 is None
), "epsilon and epsilon_0_0 cannot be set at the same time"
ret += f"variable EPSILON equal {epsilon:f}\n"
for i, j in sigma_key_index:
ret += "pair_coeff {} {} {}${{EPSILON}} {:f} {:f}\n".format(
i + 1,
j + 1,
pair_coeff_str,
sparam["sigma_" + str(i) + "_" + str(j)],
activation,
)
else:
assert epsilon_0_0 is not None, "epsilon or epsilon_0_0 must be set"
for i, j in sigma_key_index:
ret += "pair_coeff {} {} {:s}{:f} {:f} {:f}\n".format(
i + 1,
j + 1,
pair_coeff_str,
sparam["epsilon_" + str(i) + "_" + str(j)],
sparam["sigma_" + str(i) + "_" + str(j)],
activation,
)
return ret
🧰 Tools
🪛 Ruff (0.8.2)

50-55: .format call is missing argument(s) for placeholder(s): p

(F524)



def _ff_soft_on(lamb, sparam):
nn = sparam["n"]
alpha_lj = sparam["alpha_lj"]
rcut = sparam["rcut"]
epsilon = sparam["epsilon"]
# sigma = sparam['sigma']
activation = sparam["activation"]
ret = ""
ret += f"variable EPSILON equal {epsilon:f}\n"
ret += f"pair_style lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
ret = parse_lj_sigma_epsilon(ret, sparam, hybrid=False)

element_num = sparam.get("element_num", 1)
sigma_key_index = filter(
lambda t: t[0] <= t[1],
((i, j) for i in range(element_num) for j in range(element_num)),
)
for i, j in sigma_key_index:
ret += "pair_coeff {} {} ${{EPSILON}} {:f} {:f}\n".format(
i + 1,
j + 1,
sparam["sigma_" + str(i) + "_" + str(j)],
activation,
)

# ret += 'pair_coeff * * ${EPSILON} %f %f\n' % (sigma, activation)
ret += "fix tot_pot all adapt/fep 0 pair lj/cut/soft epsilon * * v_LAMBDA scale yes\n"
ret += "compute e_diff all fep ${TEMP} pair lj/cut/soft epsilon * * v_EPSILON\n"
ret += "compute lj_pe all pair lj/cut/soft\n"
ret += "variable e_diff equal c_lj_pe/v_LAMBDA\n"
return ret


def _ff_deep_on(lamb, sparam, model, if_meam=False, meam_model=None):
nn = sparam["n"]
alpha_lj = sparam["alpha_lj"]
rcut = sparam["rcut"]
epsilon = sparam["epsilon"]
# sigma = sparam['sigma']
activation = sparam["activation"]
ret = ""
ret += f"variable EPSILON equal {epsilon:f}\n"
ret += "variable ONE equal 1\n"
if if_meam:
ret += f"pair_style hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
Expand All @@ -76,20 +95,8 @@ def _ff_deep_on(lamb, sparam, model, if_meam=False, meam_model=None):
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
ret += "pair_coeff * * deepmd\n"

element_num = sparam.get("element_num", 1)
sigma_key_index = filter(
lambda t: t[0] <= t[1],
((i, j) for i in range(element_num) for j in range(element_num)),
)
for i, j in sigma_key_index:
ret += "pair_coeff {} {} lj/cut/soft ${{EPSILON}} {:f} {:f}\n".format(
i + 1,
j + 1,
sparam["sigma_" + str(i) + "_" + str(j)],
activation,
)
ret = parse_lj_sigma_epsilon(ret, sparam, hybrid=True)

# ret += 'pair_coeff * * lj/cut/soft ${EPSILON} %f %f\n' % (sigma, activation)
if if_meam:
ret += "fix tot_pot all adapt/fep 0 pair meam scale * * v_LAMBDA\n"
ret += "compute e_diff all fep ${TEMP} pair meam scale * * v_ONE\n"
Expand All @@ -98,20 +105,16 @@ def _ff_deep_on(lamb, sparam, model, if_meam=False, meam_model=None):
"fix tot_pot all adapt/fep 0 pair deepmd scale * * v_LAMBDA\n"
)
ret += "compute e_diff all fep ${TEMP} pair deepmd scale * * v_ONE\n"
ret += "variable e_diff equal c_e_diff[1]\n"
return ret


def _ff_soft_off(lamb, sparam, model, if_meam=False, meam_model=None):
nn = sparam["n"]
alpha_lj = sparam["alpha_lj"]
rcut = sparam["rcut"]
epsilon = sparam["epsilon"]
# sigma = sparam['sigma']
activation = sparam["activation"]
ret = ""
ret += "variable INV_LAMBDA equal 1-${LAMBDA}\n"
ret += f"variable EPSILON equal {epsilon:f}\n"
ret += "variable INV_EPSILON equal -${EPSILON}\n"
if if_meam:
ret += f"pair_style hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
ret += f'pair_coeff * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
Expand All @@ -120,22 +123,11 @@ def _ff_soft_off(lamb, sparam, model, if_meam=False, meam_model=None):
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
ret += "pair_coeff * * deepmd\n"

element_num = sparam.get("element_num", 1)
sigma_key_index = filter(
lambda t: t[0] <= t[1],
((i, j) for i in range(element_num) for j in range(element_num)),
)
for i, j in sigma_key_index:
ret += "pair_coeff {} {} lj/cut/soft ${{EPSILON}} {:f} {:f}\n".format(
i + 1,
j + 1,
sparam["sigma_" + str(i) + "_" + str(j)],
activation,
)
ret = parse_lj_sigma_epsilon(ret, sparam, hybrid=True)

# ret += 'pair_coeff * * lj/cut/soft ${EPSILON} %f %f\n' % (sigma, activation)
ret += "fix tot_pot all adapt/fep 0 pair lj/cut/soft epsilon * * v_INV_LAMBDA scale yes\n"
ret += "compute e_diff all fep ${TEMP} pair lj/cut/soft epsilon * * v_INV_EPSILON\n"
ret += "compute lj_pe all pair lj/cut/soft\n"
ret += "variable e_diff equal -c_lj_pe/v_INV_LAMBDA\n"
return ret


Expand Down Expand Up @@ -202,7 +194,7 @@ def _gen_lammps_input_ideal(
ret += f"timestep {timestep}\n"
ret += "compute allmsd all msd\n"
ret += "thermo ${THERMO_FREQ}\n"
ret += "thermo_style custom step ke pe etotal enthalpy temp press vol c_e_diff[1] c_allmsd[*]\n"
ret += "thermo_style custom step ke pe etotal enthalpy temp press vol v_e_diff c_allmsd[*]\n"
ret += "thermo_modify format 9 %.16e\n"
ret += "dump 1 all custom ${DUMP_FREQ} dump.hti id type x y z vx vy vz\n"
if ens == "nvt":
Expand Down
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