Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

temporarily enable and disable --unsafe-fixes #71

Merged
merged 5 commits into from
Aug 4, 2024
Merged

temporarily enable and disable --unsafe-fixes #71

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
6beff18
enable --unsafe-fixes
Yi-FanLi Aug 4, 2024
5fff4f6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 4, 2024
b446b80
NPY002 Replace legacy call with
Yi-FanLi Aug 4, 2024
a40947e
Merge branch 'upstream-pre-commit-ci-update-config' of github.com:Yi-…
Yi-FanLi Aug 4, 2024
c2cea67
disable --unsafe-fixes
Yi-FanLi Aug 4, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 8 additions & 8 deletions dpti/equi.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,19 +44,19 @@
ret += "variable THERMO_FREQ equal %d\n" % thermo_freq
ret += "variable DUMP_FREQ equal %d\n" % dump_freq
ret += "variable NREPEAT equal ${NSTEPS}/${DUMP_FREQ}\n"
ret += "variable TEMP equal %.6f\n" % temp
ret += f"variable TEMP equal {temp:.6f}\n"

Check warning on line 47 in dpti/equi.py

View check run for this annotation

Codecov / codecov/patch

dpti/equi.py#L47 

Added line #L47 was not covered by tests
# if equi_settings['pres'] is not None :
if pres is not None:
ret += "variable PRES equal %.6f\n" % pres
ret += "variable TAU_T equal %.6f\n" % tau_t
ret += "variable TAU_P equal %.6f\n" % tau_p
ret += f"variable PRES equal {pres:.6f}\n"
ret += f"variable TAU_T equal {tau_t:.6f}\n"
ret += f"variable TAU_P equal {tau_p:.6f}\n"

Check warning on line 52 in dpti/equi.py

View check run for this annotation

Codecov / codecov/patch

dpti/equi.py#L50-L52 

Added lines #L50 - L52 were not covered by tests
ret += "# ---------------------- INITIALIZAITION ------------------\n"
ret += "units metal\n"
ret += "boundary p p p\n"
ret += "atom_style atomic\n"
ret += "# --------------------- ATOM DEFINITION ------------------\n"
ret += "box tilt large\n"
ret += "read_data %s\n" % equi_conf
ret += f"read_data {equi_conf}\n"

Check warning on line 59 in dpti/equi.py

View check run for this annotation

Codecov / codecov/patch

dpti/equi.py#L59 

Added line #L59 was not covered by tests
ret += "change_box all triclinic\n"
for jj in range(len(mass_map)):
ret += "mass %d %.6f\n" % (jj + 1, mass_map[jj])
Expand All @@ -82,7 +82,7 @@
ret = ""
ret += "# --------------------- FORCE FIELDS ---------------------\n"
if not if_meam:
ret += "pair_style deepmd %s\n" % model
ret += f"pair_style deepmd {model}\n"

Check warning on line 85 in dpti/equi.py

View check run for this annotation

Codecov / codecov/patch

dpti/equi.py#L85 

Added line #L85 was not covered by tests
ret += "pair_coeff * *\n"
else:
meam_library = meam_model["library"]
Expand All @@ -97,7 +97,7 @@
ret = ""
ret += "# --------------------- MD SETTINGS ----------------------\n"
ret += "neighbor 1.0 bin\n"
ret += "timestep %.6f\n" % timestep
ret += f"timestep {timestep:.6f}\n"

Check warning on line 100 in dpti/equi.py

View check run for this annotation

Codecov / codecov/patch

dpti/equi.py#L100 

Added line #L100 was not covered by tests
ret += "thermo ${THERMO_FREQ}\n"
ret += "compute allmsd all msd\n"
ret += "thermo_style custom step ke pe etotal enthalpy temp press vol lx ly lz xy xz yz pxx pyy pzz pxy pxz pyz c_allmsd[*]\n"
Expand Down Expand Up @@ -132,7 +132,7 @@
elif ens == "nve":
ret += "fix 1 all nve\n"
else:
raise RuntimeError("unknow ensemble %s\n" % ens)
raise RuntimeError(f"unknow ensemble {ens}\n")

Check warning on line 135 in dpti/equi.py

View check run for this annotation

Codecov / codecov/patch

dpti/equi.py#L135 

Added line #L135 was not covered by tests
ret += "fix mzero all momentum 10 linear 1 1 1\n"
ret += "# --------------------- INITIALIZE -----------------------\n"
ret += "velocity all create ${TEMP} %d\n" % (
Expand Down
32 changes: 16 additions & 16 deletions dpti/hti.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@
# sigma_hh = sparam['sigma_hh']
activation = sparam["activation"]
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 46 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L46 

Added line #L46 was not covered by tests
ret += f"pair_style lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

element_num = sparam.get("element_num", 1)
Expand Down Expand Up @@ -79,7 +79,7 @@
# sigma_hh = sparam['sigma_hh']
activation = sparam["activation"]
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 82 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L82 

Added line #L82 was not covered by tests
ret += "variable ONE equal 1\n"
# if if_meam:
# ret += 'pair_style hybrid/overlay meam lj/cut/soft %f %f %f \n' % (nn, alpha_lj, rcut)
Expand Down Expand Up @@ -166,7 +166,7 @@
# sigma_hh = sparam['sigma_hh']
activation = sparam["activation"]
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 169 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L169 

Added line #L169 was not covered by tests
ret += "variable INV_EPSILON equal -${EPSILON}\n"
# if if_meam:
# ret += 'pair_style hybrid/overlay meam lj/cut/soft %f %f %f \n' % (nn, alpha_lj, rcut)
Expand Down Expand Up @@ -248,7 +248,7 @@
sum_str = "f_l_spring_1"
for ii in range(1, ntypes):
sum_str += "+f_l_spring_%s" % (ii + 1)
ret += "variable l_spring equal %s\n" % (sum_str)
ret += f"variable l_spring equal {sum_str}\n"

Check warning on line 251 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L251 

Added line #L251 was not covered by tests
return ret


Expand Down Expand Up @@ -277,7 +277,7 @@
def _ff_two_steps(lamb, model, m_spring_k, step):
ret = ""
ret += "# --------------------- FORCE FIELDS ---------------------\n"
ret += "pair_style deepmd %s\n" % model
ret += f"pair_style deepmd {model}\n"

Check warning on line 280 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L280 

Added line #L280 was not covered by tests
ret += "pair_coeff * *\n"

if step == "both" or step == "spring_off":
Expand Down Expand Up @@ -330,19 +330,19 @@
ret += "variable NSTEPS equal %d\n" % nsteps
ret += "variable THERMO_FREQ equal %d\n" % thermo_freq
ret += "variable DUMP_FREQ equal %d\n" % dump_freq
ret += "variable TEMP equal %f\n" % temp
ret += "variable PRES equal %f\n" % pres
ret += "variable TAU_T equal %f\n" % tau_t
ret += "variable TAU_P equal %f\n" % tau_p
ret += "variable LAMBDA equal %.10e\n" % lamb
ret += f"variable TEMP equal {temp:f}\n"
ret += f"variable PRES equal {pres:f}\n"
ret += f"variable TAU_T equal {tau_t:f}\n"
ret += f"variable TAU_P equal {tau_p:f}\n"
ret += f"variable LAMBDA equal {lamb:.10e}\n"

Check warning on line 337 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L333-L337 

Added lines #L333 - L337 were not covered by tests
ret += "variable INV_LAMBDA equal %.10e\n" % (1 - lamb)
ret += "# ---------------------- INITIALIZAITION ------------------\n"
ret += "units metal\n"
ret += "boundary p p p\n"
ret += "atom_style atomic\n"
ret += "# --------------------- ATOM DEFINITION ------------------\n"
ret += "box tilt large\n"
ret += "read_data %s\n" % conf_file
ret += f"read_data {conf_file}\n"

Check warning on line 345 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L345 

Added line #L345 was not covered by tests
if copies is not None:
ret += "replicate %d %d %d\n" % (copies[0], copies[1], copies[2])
ret += "change_box all triclinic\n"
Expand All @@ -367,7 +367,7 @@

ret += "# --------------------- MD SETTINGS ----------------------\n"
ret += "neighbor 1.0 bin\n"
ret += "timestep %s\n" % timestep
ret += f"timestep {timestep}\n"

Check warning on line 370 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L370 

Added line #L370 was not covered by tests
ret += "thermo ${THERMO_FREQ}\n"
ret += "compute allmsd all msd\n"
if 1 - lamb != 0:
Expand Down Expand Up @@ -405,7 +405,7 @@
elif ens == "nve":
ret += "fix 1 all nve\n"
else:
raise RuntimeError("unknow ensemble %s\n" % ens)
raise RuntimeError(f"unknow ensemble {ens}\n")

Check warning on line 408 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L408 

Added line #L408 was not covered by tests
ret += "# --------------------- INITIALIZE -----------------------\n"
ret += "velocity all create ${TEMP} %d\n" % (
np.random.default_rng().integers(1, 2**16)
Expand Down Expand Up @@ -806,7 +806,7 @@
from_ti = os.path.join(from_task, "hti.out")
if not os.path.isfile(from_ti):
raise RuntimeError(
"cannot find file %s, task should be computed befor refined" % from_ti
f"cannot find file {from_ti}, task should be computed befor refined"
)
tmp_array = np.loadtxt(from_ti)
all_t = tmp_array[:, 0]
Expand Down Expand Up @@ -1276,9 +1276,9 @@
info = thermo_info.copy()

if jdata["reference"] == "einstein":
print("# free ener of Einstein Mole: %20.8f" % e0)
print(f"# free ener of Einstein Mole: {e0:20.8f}")

Check warning on line 1279 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L1279 

Added line #L1279 was not covered by tests
else:
print("# free ener of ideal gas: %20.8f" % e0)
print(f"# free ener of ideal gas: {e0:20.8f}")

Check warning on line 1281 in dpti/hti.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti.py#L1281 

Added line #L1281 was not covered by tests

print(
("# fe contrib due to integration " + print_format) % (de, de_err[0], de_err[1])
Expand Down
6 changes: 3 additions & 3 deletions dpti/hti_ice.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -223,14 +223,14 @@
print_format = "%20.12f %10.3e %10.3e"
hti.print_thermo_info(thermo_info)
if crystal == "vega":
print("# free ener of Einstein Mole: %20.8f" % (e0))
print(f"# free ener of Einstein Mole: {e0:20.8f}")

Check warning on line 226 in dpti/hti_ice.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_ice.py#L226 

Added line #L226 was not covered by tests
else:
print("# free ener of Einstein Crys: %20.8f" % (e0))
print(f"# free ener of Einstein Crys: {e0:20.8f}")

Check warning on line 228 in dpti/hti_ice.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_ice.py#L228 

Added line #L228 was not covered by tests
print(f"# Pauling corr {note_pauling}: {pauling_corr:20.8f}")
print(
("# fe integration " + print_format) % (de, de_err[0], de_err[1])
)
print("# fe const shift %20.12f" % args.shift)
print(f"# fe const shift {args.shift:20.12f}")

Check warning on line 233 in dpti/hti_ice.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_ice.py#L233 

Added line #L233 was not covered by tests
# if args.type == 'helmholtz' :
print("# Helmholtz free ener per mol (stat_err inte_err) [eV]:")
print(print_format % (e0 + de - args.shift, de_err[0], de_err[1]))
Expand Down
22 changes: 11 additions & 11 deletions dpti/hti_liq.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
# sigma = sparam['sigma']
activation = sparam["activation"]
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 39 in dpti/hti_liq.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_liq.py#L39 

Added line #L39 was not covered by tests
ret += f"pair_style lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

element_num = sparam.get("element_num", 1)
Expand Down Expand Up @@ -66,7 +66,7 @@
# sigma = sparam['sigma']
activation = sparam["activation"]
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 69 in dpti/hti_liq.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_liq.py#L69 

Added line #L69 was not covered by tests
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 Down Expand Up @@ -110,7 +110,7 @@
activation = sparam["activation"]
ret = ""
ret += "variable INV_LAMBDA equal 1-${LAMBDA}\n"
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 113 in dpti/hti_liq.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_liq.py#L113 

Added line #L113 was not covered by tests
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"
Expand Down Expand Up @@ -166,19 +166,19 @@
ret += "variable NSTEPS equal %d\n" % nsteps
ret += "variable THERMO_FREQ equal %d\n" % thermo_freq
ret += "variable DUMP_FREQ equal %d\n" % dump_freq
ret += "variable TEMP equal %f\n" % temp
ret += "variable PRES equal %f\n" % pres
ret += "variable TAU_T equal %f\n" % tau_t
ret += "variable TAU_P equal %f\n" % tau_p
ret += "variable LAMBDA equal %.10e\n" % lamb
ret += f"variable TEMP equal {temp:f}\n"
ret += f"variable PRES equal {pres:f}\n"
ret += f"variable TAU_T equal {tau_t:f}\n"
ret += f"variable TAU_P equal {tau_p:f}\n"
ret += f"variable LAMBDA equal {lamb:.10e}\n"

Check warning on line 173 in dpti/hti_liq.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_liq.py#L169-L173 

Added lines #L169 - L173 were not covered by tests
ret += "variable ZERO equal 0\n"
ret += "# ---------------------- INITIALIZAITION ------------------\n"
ret += "units metal\n"
ret += "boundary p p p\n"
ret += "atom_style atomic\n"
ret += "# --------------------- ATOM DEFINITION ------------------\n"
ret += "box tilt large\n"
ret += "read_data %s\n" % conf_file
ret += f"read_data {conf_file}\n"

Check warning on line 181 in dpti/hti_liq.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_liq.py#L181 

Added line #L181 was not covered by tests
if copies is not None:
ret += "replicate %d %d %d\n" % (copies[0], copies[1], copies[2])
ret += "change_box all triclinic\n"
Expand All @@ -199,7 +199,7 @@
raise RuntimeError("unknown step")
ret += "# --------------------- MD SETTINGS ----------------------\n"
ret += "neighbor 1.0 bin\n"
ret += "timestep %s\n" % timestep
ret += f"timestep {timestep}\n"

Check warning on line 202 in dpti/hti_liq.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_liq.py#L202 

Added line #L202 was not covered by tests
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"
Expand All @@ -212,7 +212,7 @@
elif ens == "nve":
ret += "fix 1 all nve\n"
else:
raise RuntimeError("unknow ensemble %s\n" % ens)
raise RuntimeError(f"unknow ensemble {ens}\n")

Check warning on line 215 in dpti/hti_liq.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_liq.py#L215 

Added line #L215 was not covered by tests
ret += "fix mzero all momentum 10 linear 1 1 1\n"
ret += "# --------------------- INITIALIZE -----------------------\n"
ret += "velocity all create ${TEMP} %d\n" % (
Expand Down
34 changes: 17 additions & 17 deletions dpti/hti_water.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,16 +40,16 @@
sigma_hh = sparam["sigma_hh"]
activation = sparam["activation"]
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 43 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L43 

Added line #L43 was not covered by tests
ret += f"pair_style lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f} \n"
ret += f"pair_coeff 1 1 ${{EPSILON}} {sigma_oo:f} {activation:f}\n"
ret += f"pair_coeff 1 2 ${{EPSILON}} {sigma_oh:f} {activation:f}\n"
ret += f"pair_coeff 2 2 ${{EPSILON}} {sigma_hh:f} {activation:f}\n"
ret += "bond_style harmonic\n"
ret += f"bond_coeff 1 {bond_k:f} {bond_l:f}\n"
ret += "variable ANGLE_K equal ${LAMBDA}*%.16e\n" % angle_k
ret += f"variable ANGLE_K equal ${{LAMBDA}}*{angle_k:.16e}\n"

Check warning on line 50 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L50 

Added line #L50 was not covered by tests
ret += "angle_style harmonic\n"
ret += "angle_coeff 1 ${ANGLE_K} %f\n" % (angle_t)
ret += f"angle_coeff 1 ${{ANGLE_K}} {angle_t:f}\n"

Check warning on line 52 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L52 

Added line #L52 was not covered by tests
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"
return ret
Expand All @@ -69,7 +69,7 @@
sigma_hh = sparam["sigma_hh"]
activation = sparam["activation"]
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 72 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L72 

Added line #L72 was not covered by tests
ret += "variable ONE equal 1\n"
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f} \n"
ret += "pair_coeff * * deepmd\n"
Expand Down Expand Up @@ -100,7 +100,7 @@
activation = sparam["activation"]
ret = ""
ret += "variable INV_LAMBDA equal 1-${LAMBDA}\n"
ret += "variable EPSILON equal %f\n" % epsilon
ret += f"variable EPSILON equal {epsilon:f}\n"

Check warning on line 103 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L103 

Added line #L103 was not covered by tests
ret += "variable INV_EPSILON equal -${EPSILON}\n"
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f} \n"
ret += "pair_coeff * * deepmd\n"
Expand All @@ -109,10 +109,10 @@
ret += f"pair_coeff 2 2 lj/cut/soft ${{EPSILON}} {sigma_hh:f} {activation:f}\n"
ret += "variable BOND_K equal %.16e\n" % (bond_k * (1 - lamb))
ret += "bond_style harmonic\n"
ret += "bond_coeff 1 ${BOND_K} %f\n" % (bond_l)
ret += f"bond_coeff 1 ${{BOND_K}} {bond_l:f}\n"

Check warning on line 112 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L112 

Added line #L112 was not covered by tests
ret += "variable ANGLE_K equal %.16e\n" % (angle_k * (1 - lamb))
ret += "angle_style harmonic\n"
ret += "angle_coeff 1 ${ANGLE_K} %f\n" % (angle_t)
ret += f"angle_coeff 1 ${{ANGLE_K}} {angle_t:f}\n"

Check warning on line 115 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L115 

Added line #L115 was not covered by tests
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"
return ret
Expand Down Expand Up @@ -143,18 +143,18 @@
ret += "variable NSTEPS equal %d\n" % nsteps
ret += "variable THERMO_FREQ equal %d\n" % prt_freq
ret += "variable DUMP_FREQ equal %d\n" % dump_freq
ret += "variable TEMP equal %f\n" % temp
ret += "variable PRES equal %f\n" % pres
ret += "variable TAU_T equal %f\n" % tau_t
ret += "variable TAU_P equal %f\n" % tau_p
ret += "variable LAMBDA equal %.10e\n" % lamb
ret += f"variable TEMP equal {temp:f}\n"
ret += f"variable PRES equal {pres:f}\n"
ret += f"variable TAU_T equal {tau_t:f}\n"
ret += f"variable TAU_P equal {tau_p:f}\n"
ret += f"variable LAMBDA equal {lamb:.10e}\n"

Check warning on line 150 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L146-L150 

Added lines #L146 - L150 were not covered by tests
ret += "# ---------------------- INITIALIZAITION ------------------\n"
ret += "units metal\n"
ret += "boundary p p p\n"
ret += "atom_style angle\n"
ret += "# --------------------- ATOM DEFINITION ------------------\n"
ret += "box tilt large\n"
ret += "read_data %s\n" % conf_file
ret += f"read_data {conf_file}\n"

Check warning on line 157 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L157 

Added line #L157 was not covered by tests
if copies is not None:
ret += "replicate %d %d %d\n" % (copies[0], copies[1], copies[2])
ret += "change_box all triclinic\n"
Expand All @@ -170,7 +170,7 @@
ret += "special_bonds lj/coul 1 1 1 angle no\n"
ret += "# --------------------- MD SETTINGS ----------------------\n"
ret += "neighbor 1.0 bin\n"
ret += "timestep %s\n" % dt
ret += f"timestep {dt}\n"

Check warning on line 173 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L173 

Added line #L173 was not covered by tests
ret += "thermo ${THERMO_FREQ}\n"
ret += "thermo_style custom step ke pe etotal enthalpy temp press vol ebond eangle c_e_diff[1]\n"
ret += "thermo_modify format 9 %.16e\n"
Expand All @@ -184,7 +184,7 @@
elif ens == "nve":
ret += "fix 1 all nve\n"
else:
raise RuntimeError("unknow ensemble %s\n" % ens)
raise RuntimeError(f"unknow ensemble {ens}\n")

Check warning on line 187 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L187 

Added line #L187 was not covered by tests
ret += "fix mzero all momentum 10 linear 1 1 1\n"
ret += "# --------------------- INITIALIZE -----------------------\n"
ret += "velocity all create ${TEMP} %d\n" % (
Expand Down Expand Up @@ -291,7 +291,7 @@
from_ti = os.path.join(from_task, "hti.out")
if not os.path.isfile(from_ti):
raise RuntimeError(
"cannot find file %s, task should be computed befor refined" % from_ti
f"cannot find file {from_ti}, task should be computed befor refined"
)
tmp_array = np.loadtxt(from_ti)
all_t = tmp_array[:, 0]
Expand Down Expand Up @@ -667,7 +667,7 @@
def post_tasks(iter_name, natoms, method="inte", scheme="s"):
subtask_name = os.path.join(iter_name, "00.angle_on")
fe = compute_ideal_mol(subtask_name)
print("# fe of ideal mol: %20.12f" % fe)
print(f"# fe of ideal mol: {fe:20.12f}")

Check warning on line 670 in dpti/hti_water.py

View check run for this annotation

Codecov / codecov/patch

dpti/hti_water.py#L670 

Added line #L670 was not covered by tests
# print('# fe of ideal gas: %20.12f' % (einstein.ideal_gas_fe(subtask_name) * 3))
if method == "inte":
e0, err0, tinfo0 = _post_tasks(subtask_name, "angle_on", natoms, scheme=scheme)
Expand Down
Loading
Loading