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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Jul 29, 2024
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36 changes: 5 additions & 31 deletions dpti/hti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,21 +85,10 @@ def _ff_deep_on(lamb, model, sparam, if_meam=False, meam_model=None):
# ret += 'pair_style hybrid/overlay meam lj/cut/soft %f %f %f \n' % (nn, alpha_lj, rcut)
# ret += 'pair_coeff * * meam /home/fengbo/4_Sn/meam_files/library_18Metal.meam Sn /home/fengbo/4_Sn/meam_files/Sn_18Metal.meam Sn \n'
if if_meam:
ret += (
"pair_style hybrid/overlay meam lj/cut/soft {:f} {:f} {:f}\n".format(
nn,
alpha_lj,
rcut,
)
)
ret += f"pair_style hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += f'pair_coeff * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
else:
ret += "pair_style hybrid/overlay deepmd {} lj/cut/soft {:f} {:f} {:f}\n".format(
model,
nn,
alpha_lj,
rcut,
)
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += "pair_coeff * * deepmd\n"

element_num = sparam.get("element_num", 1)
Expand Down Expand Up @@ -183,22 +172,11 @@ def _ff_lj_off(lamb, model, sparam, if_meam=False, meam_model=None):
# ret += 'pair_style hybrid/overlay meam lj/cut/soft %f %f %f \n' % (nn, alpha_lj, rcut)
# ret += 'pair_coeff * * meam /home/fengbo/4_Sn/meam_files/library_18Metal.meam Sn /home/fengbo/4_Sn/meam_files/Sn_18Metal.meam Sn\n'
if if_meam:
ret += (
"pair_style hybrid/overlay meam lj/cut/soft {:f} {:f} {:f}\n".format(
nn,
alpha_lj,
rcut,
)
)
ret += f"pair_style hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += f'pair_coeff * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
# ret += f'pair_coeff * * meam {meam_model[0]} {meam_model[2]} {meam_model[1]} {meam_model[2]}\n'
else:
ret += "pair_style hybrid/overlay deepmd {} lj/cut/soft {:f} {:f} {:f}\n".format(
model,
nn,
alpha_lj,
rcut,
)
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += "pair_coeff * * deepmd\n"

element_num = sparam.get("element_num", 1)
Expand Down Expand Up @@ -265,11 +243,7 @@ def _ff_spring(lamb, m_spring_k, var_spring):
m_spring_const = m_spring_k[ii] * (1 - lamb)
else:
m_spring_const = m_spring_k[ii]
ret += "fix l_spring_{} type_{} spring/self {:.10e}\n".format(
ii + 1,
ii + 1,
m_spring_const,
)
ret += f"fix l_spring_{ii + 1} type_{ii + 1} spring/self {m_spring_const:.10e}\n"

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ret += "fix_modify l_spring_%s energy yes\n" % (ii + 1)
sum_str = "f_l_spring_1"
for ii in range(1, ntypes):
Expand Down
30 changes: 4 additions & 26 deletions dpti/hti_liq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,22 +69,11 @@ def _ff_deep_on(lamb, sparam, model, if_meam=False, meam_model=None):
ret += "variable EPSILON equal %f\n" % epsilon
ret += "variable ONE equal 1\n"
if if_meam:
ret += (
"pair_style hybrid/overlay meam lj/cut/soft {:f} {:f} {:f}\n".format(
nn,
alpha_lj,
rcut,
)
)
ret += f"pair_style hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += f'pair_coeff * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
# ret += f'pair_coeff * * meam {meam_model[0]} {meam_model[2]} {meam_model[1]} {meam_model[2]}\n'
else:
ret += "pair_style hybrid/overlay deepmd {} lj/cut/soft {:f} {:f} {:f}\n".format(
model,
nn,
alpha_lj,
rcut,
)
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += "pair_coeff * * deepmd\n"

element_num = sparam.get("element_num", 1)
Expand Down Expand Up @@ -124,22 +113,11 @@ def _ff_soft_off(lamb, sparam, model, if_meam=False, meam_model=None):
ret += "variable EPSILON equal %f\n" % epsilon
ret += "variable INV_EPSILON equal -${EPSILON}\n"
if if_meam:
ret += (
"pair_style hybrid/overlay meam lj/cut/soft {:f} {:f} {:f}\n".format(
nn,
alpha_lj,
rcut,
)
)
ret += f"pair_style hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += f'pair_coeff * * meam {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
# ret += f'pair_coeff * * meam {meam_model[0]} {meam_model[2]} {meam_model[1} {meam_model[2]} \n'
else:
ret += "pair_style hybrid/overlay deepmd {} lj/cut/soft {:f} {:f} {:f}\n".format(
model,
nn,
alpha_lj,
rcut,
)
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"

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ret += "pair_coeff * * deepmd\n"

element_num = sparam.get("element_num", 1)
Expand Down
14 changes: 2 additions & 12 deletions dpti/hti_water.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,12 +71,7 @@ def _ff_deep_on(lamb, model, bparam, sparam):
ret = ""
ret += "variable EPSILON equal %f\n" % epsilon
ret += "variable ONE equal 1\n"
ret += "pair_style hybrid/overlay deepmd {} lj/cut/soft {:f} {:f} {:f} \n".format(
model,
nn,
alpha_lj,
rcut,
)
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f} \n"

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ret += "pair_coeff * * deepmd\n"
ret += f"pair_coeff 1 1 lj/cut/soft ${{EPSILON}} {sigma_oo:f} {activation:f}\n"
ret += f"pair_coeff 1 2 lj/cut/soft ${{EPSILON}} {sigma_oh:f} {activation:f}\n"
Expand Down Expand Up @@ -107,12 +102,7 @@ def _ff_bond_angle_off(lamb, model, bparam, sparam):
ret += "variable INV_LAMBDA equal 1-${LAMBDA}\n"
ret += "variable EPSILON equal %f\n" % epsilon
ret += "variable INV_EPSILON equal -${EPSILON}\n"
ret += "pair_style hybrid/overlay deepmd {} lj/cut/soft {:f} {:f} {:f} \n".format(
model,
nn,
alpha_lj,
rcut,
)
ret += f"pair_style hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f} \n"

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ret += "pair_coeff * * deepmd\n"
ret += f"pair_coeff 1 1 lj/cut/soft ${{EPSILON}} {sigma_oo:f} {activation:f}\n"
ret += f"pair_coeff 1 2 lj/cut/soft ${{EPSILON}} {sigma_oh:f} {activation:f}\n"
Expand Down
1 change: 1 addition & 0 deletions dpti/lib/ovito_file_convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
This Script is adapted from Alexander Stukowski, the author of OVITO.
See: http://forum.ovito.org/index.php?topic=131.0 for details.
"""

import argparse

from ovito.io import export_file, import_file
Expand Down
44 changes: 5 additions & 39 deletions dpti/ti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -619,21 +619,9 @@ def post_tasks(
)
for ii in range(len(all_temps)):
print(
"{:9.2f} {:20.12f} {:9.2e} {:9.2e} {:9.2e}".format(
all_temps[ii],
all_fe[ii],
all_fe_err[ii],
all_fe_sys_err[ii],
np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]),
)
)
result += "{:9.2f} {:20.12f} {:9.2e} {:9.2e} {:9.2e}\n".format(
all_temps[ii],
all_fe[ii],
all_fe_err[ii],
all_fe_sys_err[ii],
np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]),
f"{all_temps[ii]:9.2f} {all_fe[ii]:20.12f} {all_fe_err[ii]:9.2e} {all_fe_sys_err[ii]:9.2e} {np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]):9.2e}"
)
result += f"{all_temps[ii]:9.2f} {all_fe[ii]:20.12f} {all_fe_err[ii]:9.2e} {all_fe_sys_err[ii]:9.2e} {np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]):9.2e}\n"

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elif "npt" in ens:
print(
"#%8s %15s %20s %9s %9s %9s"
Expand All @@ -649,25 +637,9 @@ def post_tasks(
)
for ii in range(len(all_temps)):
print(
"{:9.2f} {:15.8e} {:20.12f} {:9.2e} {:9.2e} {:9.2e}".format(
all_temps[ii],
all_press[ii],
all_fe[ii],
all_fe_err[ii],
all_fe_sys_err[ii],
np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]),
)
)
result += (
"{:9.2f} {:15.8e} {:20.12f} {:9.2e} {:9.2e} {:9.2e}\n".format(
all_temps[ii],
all_press[ii],
all_fe[ii],
all_fe_err[ii],
all_fe_sys_err[ii],
np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]),
)
f"{all_temps[ii]:9.2f} {all_press[ii]:15.8e} {all_fe[ii]:20.12f} {all_fe_err[ii]:9.2e} {all_fe_sys_err[ii]:9.2e} {np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]):9.2e}"
)
result += f"{all_temps[ii]:9.2f} {all_press[ii]:15.8e} {all_fe[ii]:20.12f} {all_fe_err[ii]:9.2e} {all_fe_sys_err[ii]:9.2e} {np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]):9.2e}\n"

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# print(all_temps[ii], all_press[ii], all_fe[ii], all_fe_err[ii], all_fe_sys_err[ii], np.linalg.norm([all_fe_err[ii], all_fe_sys_err[ii]]))
# result_file.close()

Expand Down Expand Up @@ -817,13 +789,7 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
)
for ii in range(len(all_temps)):
print(
"{:9.2f} {:15.8e} {:20.12f} {:9.2e} {:9.2e}".format(
all_temps[ii],
all_press[ii],
all_fe[ii],
all_fe_err[ii],
all_fe_sys_err[ii],
)
f"{all_temps[ii]:9.2f} {all_press[ii]:15.8e} {all_fe[ii]:20.12f} {all_fe_err[ii]:9.2e} {all_fe_sys_err[ii]:9.2e}"
)
# info = dict(start_point_info=info0, end_point_info=info1, all_temps=list(all_temps), all_press=list(all_press),
# all_fe=list(all_fe), all_fe_err=list(all_fe_err), all_fe_sys_err=list(all_fe_sys_err))
Expand Down

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