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equi: write average position in out.lmp when if_dump_avg_posi=True #90

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Merged
Yi-FanLi merged 5 commits into from
Mar 15, 2025
Merged

equi: write average position in out.lmp when if_dump_avg_posi=True #90

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428d337
avoid reading --avg-posi from cmd line; only read it from json
Yi-FanLi Mar 15, 2025
183aa83
write average position in out.lmp if if_dump_avg_posi=True
Yi-FanLi Mar 15, 2025
c246ddb
support writing average position in out.lmp if if_dump_avg_posi=True
Yi-FanLi Mar 15, 2025
7234224
improve indentation
Yi-FanLi Mar 15, 2025
8769790
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 15, 2025
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20 changes: 9 additions & 11 deletions dpti/equi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ def gen_equi_dump_settings(if_dump_avg_posi):
return ret


def gen_equi_ensemble_settings(ens):
def gen_equi_ensemble_settings(ens, if_dump_avg_posi):
# ens = equi_settings['ens']
ret = ""
if ens == "nvt":
Expand All @@ -156,6 +156,11 @@ def gen_equi_ensemble_settings(ens):
ret += "velocity all zero linear\n"
ret += "# --------------------- RUN ------------------------------\n"
ret += "run ${NSTEPS}\n"
if if_dump_avg_posi:
ret += "undump fp\n"
ret += "undump 1\n"
ret += "unfix ap\n"
ret += "read_dump dump.avgposi ${NSTEPS} x y z label x f_ap[1] label y f_ap[2] label z f_ap[3]\n"
ret += "write_data out.lmp\n"
return ret

Expand Down Expand Up @@ -198,7 +203,9 @@ def gen_equi_lammps_input(
)
equi_thermo_settings = gen_equi_thermo_settings(timestep=timestep)
equi_dump_settings = gen_equi_dump_settings(if_dump_avg_posi=if_dump_avg_posi)
equi_ensemble_settings = gen_equi_ensemble_settings(ens=ens)
equi_ensemble_settings = gen_equi_ensemble_settings(
ens=ens, if_dump_avg_posi=if_dump_avg_posi
)

equi_lammps_input = (
equi_header
Expand Down Expand Up @@ -355,7 +362,6 @@ def make_task(
ens=None,
temp=None,
pres=None,
if_dump_avg_posi=None,
npt_dir=None,
):
equi_args = [
Expand Down Expand Up @@ -385,7 +391,6 @@ def make_task(
ens=ens,
temp=temp,
pres=pres,
if_dump_avg_posi=if_dump_avg_posi,
npt_dir=npt_dir,
)

Expand Down Expand Up @@ -673,12 +678,6 @@ def add_subparsers(module_subparsers):
parser_gen.add_argument(
"-p", "--pressure", type=float, help="the pressure of the system"
)
parser_gen.add_argument(
"-a",
"--avg-posi",
action="store_true",
help="dump the average position of atoms",
)
parser_gen.add_argument(
"-c", "--conf-npt", type=str, help="use conf computed from NPT simulation"
)
Expand Down Expand Up @@ -728,7 +727,6 @@ def handle_gen(args):
args.ensemble,
args.temperature,
args.pressure,
args.avg_posi,
args.conf_npt,
)

Expand Down
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