From ab60070a62a2f0a41432eba8b73cada61de1142d Mon Sep 17 00:00:00 2001
From: "C. Thang Nguyen" <thangckt@gmail.com>
Date: Thu, 11 Dec 2025 18:24:57 +0900
Subject: [PATCH 1/9] Refactor string formatting to f-strings in ti.py

Replaced old-style string formatting with f-strings throughout dpti/ti.py for improved readability and consistency. Also reformatted some function signatures and print statements for clarity and conciseness.
---
 dpti/ti.py | 124 +++++++++++++++++------------------------------------
 1 file changed, 39 insertions(+), 85 deletions(-)

diff --git a/dpti/ti.py b/dpti/ti.py
index c130475f..2e55788f 100755
--- a/dpti/ti.py
+++ b/dpti/ti.py
@@ -29,7 +29,7 @@
 
 
 def make_iter_name(iter_index):
-    return "task_ti." + ("%04d" % iter_index)
+    return f"task_ti.{iter_index:04d}"
 
 
 def parse_seq_ginv(seq):
@@ -65,9 +65,9 @@ def _gen_lammps_input(
     ret = ""
     ret += "clear\n"
     ret += "# --------------------- VARIABLES-------------------------\n"
-    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 += f"variable        NSTEPS          equal {int(nsteps)}\n"
+    ret += f"variable        THERMO_FREQ     equal {int(thermo_freq)}\n"
+    ret += f"variable        DUMP_FREQ       equal {int(dump_freq)}\n"
     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"
@@ -83,17 +83,17 @@ def _gen_lammps_input(
     ret += "box             tilt large\n"
     ret += f"read_data       {conf_file}\n"
     if copies is not None:
-        ret += "replicate       %d %d %d\n" % (copies[0], copies[1], copies[2])
+        ret += f"replicate       {int(copies[0])} {int(copies[1])} {int(copies[2])}\n"
     ret += "change_box      all triclinic\n"
     for jj in range(len(mass_map)):
-        ret += "mass            %d %f\n" % (jj + 1, mass_map[jj])
+        ret += f"mass            {jj + 1} {mass_map[jj]:f}\n"
     ret += "# --------------------- FORCE FIELDS ---------------------\n"
     # if if_meam:
     #     ret += 'pair_style      meam \n'
     #     ret += 'pair_coeff      * * /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      meam\n"
-        ret += f'pair_coeff      * * {meam_model["library"]} {meam_model["element"]} {meam_model["potential"]} {meam_model["element"]}\n'
+        ret += f"pair_coeff      * * {meam_model['library']} {meam_model['element']} {meam_model['potential']} {meam_model['element']}\n"
     else:
         if append:
             ret += f"pair_style      deepmd {model:s} {append:s}\n"
@@ -118,11 +118,15 @@ def _gen_lammps_input(
     if ens == "nvt":
         ret += "fix             1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}\n"
     elif ens == "npt-iso" or ens == "npt":
-        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
+        ret += (
+            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
+        )
     elif ens == "npt-aniso":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-tri":
-        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
+        ret += (
+            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
+        )
     elif ens == "npt-xy":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P} couple xy\n"
     elif ens == "nve":
@@ -131,9 +135,7 @@ def _gen_lammps_input(
         raise RuntimeError(f"unknow ensemble {ens}\n")
     ret += "fix             mzero all momentum 10 linear 1 1 1\n"
     ret += "# --------------------- INITIALIZE -----------------------\n"
-    ret += "velocity        all create ${TEMP} %d\n" % (
-        np.random.default_rng().integers(1, 2**16)
-    )
+    ret += f"velocity        all create ${{TEMP}} {np.random.default_rng().integers(1, 2**16)}\n"
     ret += "velocity        all zero linear\n"
     ret += "# --------------------- RUN ------------------------------\n"
     ret += "run             ${NSTEPS}\n"
@@ -163,9 +165,7 @@ def make_tasks(iter_name, jdata, if_meam=None):
     timestep = get_first_matched_key_from_dict(jdata, ["timestep", "dt"])
     # thermo_freq = jdata['thermo_freq']
     thermo_freq = get_first_matched_key_from_dict(jdata, ["thermo_freq", "stat_freq"])
-    dump_freq = get_first_matched_key_from_dict(
-        jdata, ["dump_freq", "thermo_freq", "stat_freq"]
-    )
+    dump_freq = get_first_matched_key_from_dict(jdata, ["dump_freq", "thermo_freq", "stat_freq"])
     # thermos = jdata['thermos']
     ens = jdata["ens"]
     path = jdata["path"]
@@ -242,7 +242,7 @@ def make_tasks(iter_name, jdata, if_meam=None):
         json.dump(ti_settings, f, indent=4)
 
     for ii in range(ntasks):
-        task_dir = os.path.join(job_abs_dir, "task.%06d" % ii)
+        task_dir = os.path.join(job_abs_dir, f"task.{ii:06d}")
         task_abs_dir = create_path(task_dir)
         # os.chdir(work_path)
 
@@ -373,9 +373,7 @@ def _print_thermo_info(info, more_head=""):
     print(ptr)
 
 
-def _thermo_inte(
-    jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None
-):
+def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None):
     path = jdata["path"]
     ens = jdata["ens"]
     all_temps = []
@@ -410,9 +408,7 @@ def _thermo_inte(
 
     #     return np.asarray(all_temps), np.asarray(all_press), np.asarray(all_fe), np.asarray(all_fe_err), np.asarray(all_fe_sys_err)
 
-    all_t, inte, inte_e, stat_e = integrate_range(
-        all_t, integrand, integrand_err, scheme
-    )
+    all_t, inte, inte_e, stat_e = integrate_range(all_t, integrand, integrand_err, scheme)
     for ii in range(0, len(all_t)):
         diff_e = inte[ii]
         err = stat_e[ii]
@@ -426,9 +422,7 @@ def _thermo_inte(
             sys_err *= all_t[ii]
             all_temps.append(all_t[ii])
             if "npt" in ens:
-                all_press.append(
-                    get_first_matched_key_from_dict(jdata, ["pres", "press"])
-                )
+                all_press.append(get_first_matched_key_from_dict(jdata, ["pres", "press"]))
         elif path == "p":
             e1 = Eo + diff_e
             err = np.sqrt(np.square(Eo_err) + np.square(err))
@@ -446,9 +440,7 @@ def _thermo_inte(
     )
 
 
-def post_tasks(
-    iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0
-):
+def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0):
     equi_conf = get_task_file_abspath(iter_name, jdata["equi_conf"])
     if natoms is None:
         natoms = get_natoms(equi_conf)
@@ -491,7 +483,7 @@ def post_tasks(
         print("# TI in NPT along P path")
     else:
         raise RuntimeError("invalid ens or path setting")
-    print("# natoms: %d" % natoms)
+    print(f"# natoms: {natoms:d}")
 
     for ii in all_tasks:
         # get T or P
@@ -557,9 +549,7 @@ def post_tasks(
         header="t/p Integrand U/V U/V_err enthalpy msd_xyz",
     )
 
-    info0 = _compute_thermo(
-        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
-    )
+    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -588,18 +578,14 @@ def post_tasks(
             all_fe_1,
             all_fe_err_1,
             all_fe_sys_err_1,
-        ) = _thermo_inte(
-            jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme
-        )
+        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme)
         (
             all_temps_2,
             all_press_2,
             all_fe_2,
             all_fe_err_2,
             all_fe_sys_err_2,
-        ) = _thermo_inte(
-            jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme
-        )
+        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme)
         all_temps_1 = np.flip(all_temps_1, 0)
         all_press_1 = np.flip(all_press_1, 0)
         all_fe_1 = np.flip(all_fe_1, 0)
@@ -626,17 +612,8 @@ def post_tasks(
     result = ""
     # result_file = open(f"{iter_name}/../result", 'w')
     if "nvt" == ens:
-        print(
-            "#%8s  %20s  %9s  %9s  %9s"
-            % ("T(ctrl)", "F", "stat_err", "inte_err", "err")
-        )
-        result += "#%8s  %20s  %9s  %9s  %9s\n" % (
-            "T(ctrl)",
-            "F",
-            "stat_err",
-            "inte_err",
-            "err",
-        )
+        print(f"#{'T(ctrl)':8}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}")
+        result += f"#{'T(ctrl)':8}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -644,16 +621,10 @@ def post_tasks(
             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"
     elif "npt" in ens:
         print(
-            "#%8s  %15s  %20s  %9s  %9s  %9s"
-            % ("T(ctrl)", "P(ctrl)", "F", "stat_err", "inte_err", "err")
+            f"#{'T(ctrl)':8}  {'P(ctrl)':15}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}"
         )
-        result += "#%8s  %15s  %20s  %9s  %9s  %9s\n" % (
-            "T(ctrl)",
-            "P(ctrl)",
-            "F",
-            "stat_err",
-            "inte_err",
-            "err",
+        result += (
+            f"#{'T(ctrl)':8}  {'P(ctrl)':15}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
         )
         for ii in range(len(all_temps)):
             print(
@@ -713,7 +684,7 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
         print("# TI in NPT along P path")
     else:
         raise RuntimeError("invalid ens or path setting")
-    print("# natoms: %d" % natoms)
+    print(f"# natoms: {natoms:d}")
 
     all_t = []
     for ii in all_tasks:
@@ -755,9 +726,7 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
             ukn = np.concatenate((ukn, block_u), axis=1)
     nk = np.array(nk)
 
-    info0 = _compute_thermo(
-        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
-    )
+    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -797,16 +766,13 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
         all_fe_sys_err.append(sys_err)
 
     if "nvt" == ens:
-        print("#%8s  %15s  %9s  %9s" % ("T(ctrl)", "F", "stat_err", "inte_err"))
+        print(f"#{'T(ctrl)':>8}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}")
         for ii in range(len(all_temps)):
             print(
                 f"{all_temps[ii]:9.2f}  {all_fe[ii]:20.12f}  {all_fe_err[ii]:9.2e}  {all_fe_sys_err[ii]:9.2e}"
             )
     elif "npt" in ens:
-        print(
-            "#%8s  %15s  %15s  %9s  %9s"
-            % ("T(ctrl)", "P(ctrl)", "F", "stat_err", "inte_err")
-        )
+        print(f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}")
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -828,9 +794,7 @@ def refine_task(from_task, to_task, err):
 
     from_ti = os.path.join(from_task, "ti.out")
     if not os.path.isfile(from_ti):
-        raise RuntimeError(
-            f"cannot find file {from_ti}, task should be computed befor refined"
-        )
+        raise RuntimeError(f"cannot find file {from_ti}, task should be computed befor refined")
     tmp_array = np.loadtxt(from_ti)
     all_t = tmp_array[:, 0]
     integrand = tmp_array[:, 1]
@@ -960,9 +924,7 @@ def add_module_subparsers(main_subparsers):
     )
     parser_gen.set_defaults(func=handle_gen)
 
-    parser_compute = module_subparsers.add_parser(
-        "compute", help="Compute the result of a job"
-    )
+    parser_compute = module_subparsers.add_parser("compute", help="Compute the result of a job")
     parser_compute.add_argument("JOB", type=str, help="folder of the job")
     parser_compute.add_argument(
         "-m",
@@ -1001,15 +963,9 @@ def add_module_subparsers(main_subparsers):
     )
     parser_compute.set_defaults(func=handle_compute)
 
-    parser_refine = module_subparsers.add_parser(
-        "refine", help="Refine the grid of a job"
-    )
-    parser_refine.add_argument(
-        "-i", "--input", type=str, required=True, help="input job"
-    )
-    parser_refine.add_argument(
-        "-o", "--output", type=str, required=True, help="output job"
-    )
+    parser_refine = module_subparsers.add_parser("refine", help="Refine the grid of a job")
+    parser_refine.add_argument("-i", "--input", type=str, required=True, help="input job")
+    parser_refine.add_argument("-o", "--output", type=str, required=True, help="output job")
     parser_refine.add_argument(
         "-e", "--error", type=float, required=True, help="the error required"
     )
@@ -1049,9 +1005,7 @@ def handle_compute(args):
                 raise ValueError("Cannot find temperature in hti's input json file")
         elif path == "p":
             try:
-                args.To = get_first_matched_key_from_dict(
-                    jdata_hti_in, ["pres", "press"]
-                )
+                args.To = get_first_matched_key_from_dict(jdata_hti_in, ["pres", "press"])
             except KeyError:
                 args.To = None
             if args.To is None:

From e87ebc9cfeab8aa85491573f326b58d1676f71b0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Dec 2025 09:27:26 +0000
Subject: [PATCH 2/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dpti/ti.py | 80 ++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 54 insertions(+), 26 deletions(-)

diff --git a/dpti/ti.py b/dpti/ti.py
index 2e55788f..5be88395 100755
--- a/dpti/ti.py
+++ b/dpti/ti.py
@@ -118,15 +118,11 @@ def _gen_lammps_input(
     if ens == "nvt":
         ret += "fix             1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}\n"
     elif ens == "npt-iso" or ens == "npt":
-        ret += (
-            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
-        )
+        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-aniso":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-tri":
-        ret += (
-            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
-        )
+        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-xy":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P} couple xy\n"
     elif ens == "nve":
@@ -165,7 +161,9 @@ def make_tasks(iter_name, jdata, if_meam=None):
     timestep = get_first_matched_key_from_dict(jdata, ["timestep", "dt"])
     # thermo_freq = jdata['thermo_freq']
     thermo_freq = get_first_matched_key_from_dict(jdata, ["thermo_freq", "stat_freq"])
-    dump_freq = get_first_matched_key_from_dict(jdata, ["dump_freq", "thermo_freq", "stat_freq"])
+    dump_freq = get_first_matched_key_from_dict(
+        jdata, ["dump_freq", "thermo_freq", "stat_freq"]
+    )
     # thermos = jdata['thermos']
     ens = jdata["ens"]
     path = jdata["path"]
@@ -373,7 +371,9 @@ def _print_thermo_info(info, more_head=""):
     print(ptr)
 
 
-def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None):
+def _thermo_inte(
+    jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None
+):
     path = jdata["path"]
     ens = jdata["ens"]
     all_temps = []
@@ -408,7 +408,9 @@ def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s",
 
     #     return np.asarray(all_temps), np.asarray(all_press), np.asarray(all_fe), np.asarray(all_fe_err), np.asarray(all_fe_sys_err)
 
-    all_t, inte, inte_e, stat_e = integrate_range(all_t, integrand, integrand_err, scheme)
+    all_t, inte, inte_e, stat_e = integrate_range(
+        all_t, integrand, integrand_err, scheme
+    )
     for ii in range(0, len(all_t)):
         diff_e = inte[ii]
         err = stat_e[ii]
@@ -422,7 +424,9 @@ def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s",
             sys_err *= all_t[ii]
             all_temps.append(all_t[ii])
             if "npt" in ens:
-                all_press.append(get_first_matched_key_from_dict(jdata, ["pres", "press"]))
+                all_press.append(
+                    get_first_matched_key_from_dict(jdata, ["pres", "press"])
+                )
         elif path == "p":
             e1 = Eo + diff_e
             err = np.sqrt(np.square(Eo_err) + np.square(err))
@@ -440,7 +444,9 @@ def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s",
     )
 
 
-def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0):
+def post_tasks(
+    iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0
+):
     equi_conf = get_task_file_abspath(iter_name, jdata["equi_conf"])
     if natoms is None:
         natoms = get_natoms(equi_conf)
@@ -549,7 +555,9 @@ def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="sim
         header="t/p Integrand U/V U/V_err enthalpy msd_xyz",
     )
 
-    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
+    info0 = _compute_thermo(
+        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
+    )
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -578,14 +586,18 @@ def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="sim
             all_fe_1,
             all_fe_err_1,
             all_fe_sys_err_1,
-        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme)
+        ) = _thermo_inte(
+            jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme
+        )
         (
             all_temps_2,
             all_press_2,
             all_fe_2,
             all_fe_err_2,
             all_fe_sys_err_2,
-        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme)
+        ) = _thermo_inte(
+            jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme
+        )
         all_temps_1 = np.flip(all_temps_1, 0)
         all_press_1 = np.flip(all_press_1, 0)
         all_fe_1 = np.flip(all_fe_1, 0)
@@ -613,7 +625,9 @@ def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="sim
     # result_file = open(f"{iter_name}/../result", 'w')
     if "nvt" == ens:
         print(f"#{'T(ctrl)':8}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}")
-        result += f"#{'T(ctrl)':8}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
+        result += (
+            f"#{'T(ctrl)':8}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
+        )
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -623,9 +637,7 @@ def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="sim
         print(
             f"#{'T(ctrl)':8}  {'P(ctrl)':15}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}"
         )
-        result += (
-            f"#{'T(ctrl)':8}  {'P(ctrl)':15}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
-        )
+        result += f"#{'T(ctrl)':8}  {'P(ctrl)':15}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -726,7 +738,9 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
             ukn = np.concatenate((ukn, block_u), axis=1)
     nk = np.array(nk)
 
-    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
+    info0 = _compute_thermo(
+        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
+    )
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -772,7 +786,9 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
                 f"{all_temps[ii]:9.2f}  {all_fe[ii]:20.12f}  {all_fe_err[ii]:9.2e}  {all_fe_sys_err[ii]:9.2e}"
             )
     elif "npt" in ens:
-        print(f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}")
+        print(
+            f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}"
+        )
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -794,7 +810,9 @@ def refine_task(from_task, to_task, err):
 
     from_ti = os.path.join(from_task, "ti.out")
     if not os.path.isfile(from_ti):
-        raise RuntimeError(f"cannot find file {from_ti}, task should be computed befor refined")
+        raise RuntimeError(
+            f"cannot find file {from_ti}, task should be computed befor refined"
+        )
     tmp_array = np.loadtxt(from_ti)
     all_t = tmp_array[:, 0]
     integrand = tmp_array[:, 1]
@@ -924,7 +942,9 @@ def add_module_subparsers(main_subparsers):
     )
     parser_gen.set_defaults(func=handle_gen)
 
-    parser_compute = module_subparsers.add_parser("compute", help="Compute the result of a job")
+    parser_compute = module_subparsers.add_parser(
+        "compute", help="Compute the result of a job"
+    )
     parser_compute.add_argument("JOB", type=str, help="folder of the job")
     parser_compute.add_argument(
         "-m",
@@ -963,9 +983,15 @@ def add_module_subparsers(main_subparsers):
     )
     parser_compute.set_defaults(func=handle_compute)
 
-    parser_refine = module_subparsers.add_parser("refine", help="Refine the grid of a job")
-    parser_refine.add_argument("-i", "--input", type=str, required=True, help="input job")
-    parser_refine.add_argument("-o", "--output", type=str, required=True, help="output job")
+    parser_refine = module_subparsers.add_parser(
+        "refine", help="Refine the grid of a job"
+    )
+    parser_refine.add_argument(
+        "-i", "--input", type=str, required=True, help="input job"
+    )
+    parser_refine.add_argument(
+        "-o", "--output", type=str, required=True, help="output job"
+    )
     parser_refine.add_argument(
         "-e", "--error", type=float, required=True, help="the error required"
     )
@@ -1005,7 +1031,9 @@ def handle_compute(args):
                 raise ValueError("Cannot find temperature in hti's input json file")
         elif path == "p":
             try:
-                args.To = get_first_matched_key_from_dict(jdata_hti_in, ["pres", "press"])
+                args.To = get_first_matched_key_from_dict(
+                    jdata_hti_in, ["pres", "press"]
+                )
             except KeyError:
                 args.To = None
             if args.To is None:

From ae6d27207ddd417a232c369acce13b25af04aa79 Mon Sep 17 00:00:00 2001
From: "C. Thang Nguyen" <thangckt@gmail.com>
Date: Thu, 11 Dec 2025 18:34:28 +0900
Subject: [PATCH 3/9] Update dpti/ti.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 dpti/ti.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dpti/ti.py b/dpti/ti.py
index 5be88395..41b712bc 100755
--- a/dpti/ti.py
+++ b/dpti/ti.py
@@ -83,7 +83,7 @@ def _gen_lammps_input(
     ret += "box             tilt large\n"
     ret += f"read_data       {conf_file}\n"
     if copies is not None:
-        ret += f"replicate       {int(copies[0])} {int(copies[1])} {int(copies[2])}\n"
+        ret += f"replicate       {copies[0]:d} {copies[1]:d} {copies[2]:d}\n"
     ret += "change_box      all triclinic\n"
     for jj in range(len(mass_map)):
         ret += f"mass            {jj + 1} {mass_map[jj]:f}\n"

From 1da39e54ffc123c798c695f81ea1a7d6171cf682 Mon Sep 17 00:00:00 2001
From: "C. Thang Nguyen" <thangckt@gmail.com>
Date: Thu, 11 Dec 2025 18:40:01 +0900
Subject: [PATCH 4/9] Update ti.py

---
 dpti/ti.py | 88 ++++++++++++++++++------------------------------------
 1 file changed, 29 insertions(+), 59 deletions(-)

diff --git a/dpti/ti.py b/dpti/ti.py
index 41b712bc..5f2b385e 100755
--- a/dpti/ti.py
+++ b/dpti/ti.py
@@ -65,9 +65,9 @@ def _gen_lammps_input(
     ret = ""
     ret += "clear\n"
     ret += "# --------------------- VARIABLES-------------------------\n"
-    ret += f"variable        NSTEPS          equal {int(nsteps)}\n"
-    ret += f"variable        THERMO_FREQ     equal {int(thermo_freq)}\n"
-    ret += f"variable        DUMP_FREQ       equal {int(dump_freq)}\n"
+    ret += f"variable        NSTEPS          equal {nsteps:d}\n"
+    ret += f"variable        THERMO_FREQ     equal {thermo_freq:d}\n"
+    ret += f"variable        DUMP_FREQ       equal {dump_freq:d}\n"
     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"
@@ -118,11 +118,15 @@ def _gen_lammps_input(
     if ens == "nvt":
         ret += "fix             1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}\n"
     elif ens == "npt-iso" or ens == "npt":
-        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
+        ret += (
+            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
+        )
     elif ens == "npt-aniso":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-tri":
-        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
+        ret += (
+            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
+        )
     elif ens == "npt-xy":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P} couple xy\n"
     elif ens == "nve":
@@ -161,9 +165,7 @@ def make_tasks(iter_name, jdata, if_meam=None):
     timestep = get_first_matched_key_from_dict(jdata, ["timestep", "dt"])
     # thermo_freq = jdata['thermo_freq']
     thermo_freq = get_first_matched_key_from_dict(jdata, ["thermo_freq", "stat_freq"])
-    dump_freq = get_first_matched_key_from_dict(
-        jdata, ["dump_freq", "thermo_freq", "stat_freq"]
-    )
+    dump_freq = get_first_matched_key_from_dict(jdata, ["dump_freq", "thermo_freq", "stat_freq"])
     # thermos = jdata['thermos']
     ens = jdata["ens"]
     path = jdata["path"]
@@ -371,9 +373,7 @@ def _print_thermo_info(info, more_head=""):
     print(ptr)
 
 
-def _thermo_inte(
-    jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None
-):
+def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None):
     path = jdata["path"]
     ens = jdata["ens"]
     all_temps = []
@@ -408,9 +408,7 @@ def _thermo_inte(
 
     #     return np.asarray(all_temps), np.asarray(all_press), np.asarray(all_fe), np.asarray(all_fe_err), np.asarray(all_fe_sys_err)
 
-    all_t, inte, inte_e, stat_e = integrate_range(
-        all_t, integrand, integrand_err, scheme
-    )
+    all_t, inte, inte_e, stat_e = integrate_range(all_t, integrand, integrand_err, scheme)
     for ii in range(0, len(all_t)):
         diff_e = inte[ii]
         err = stat_e[ii]
@@ -424,9 +422,7 @@ def _thermo_inte(
             sys_err *= all_t[ii]
             all_temps.append(all_t[ii])
             if "npt" in ens:
-                all_press.append(
-                    get_first_matched_key_from_dict(jdata, ["pres", "press"])
-                )
+                all_press.append(get_first_matched_key_from_dict(jdata, ["pres", "press"]))
         elif path == "p":
             e1 = Eo + diff_e
             err = np.sqrt(np.square(Eo_err) + np.square(err))
@@ -444,9 +440,7 @@ def _thermo_inte(
     )
 
 
-def post_tasks(
-    iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0
-):
+def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0):
     equi_conf = get_task_file_abspath(iter_name, jdata["equi_conf"])
     if natoms is None:
         natoms = get_natoms(equi_conf)
@@ -555,9 +549,7 @@ def post_tasks(
         header="t/p Integrand U/V U/V_err enthalpy msd_xyz",
     )
 
-    info0 = _compute_thermo(
-        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
-    )
+    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -586,18 +578,14 @@ def post_tasks(
             all_fe_1,
             all_fe_err_1,
             all_fe_sys_err_1,
-        ) = _thermo_inte(
-            jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme
-        )
+        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme)
         (
             all_temps_2,
             all_press_2,
             all_fe_2,
             all_fe_err_2,
             all_fe_sys_err_2,
-        ) = _thermo_inte(
-            jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme
-        )
+        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme)
         all_temps_1 = np.flip(all_temps_1, 0)
         all_press_1 = np.flip(all_press_1, 0)
         all_fe_1 = np.flip(all_fe_1, 0)
@@ -624,10 +612,8 @@ def post_tasks(
     result = ""
     # result_file = open(f"{iter_name}/../result", 'w')
     if "nvt" == ens:
-        print(f"#{'T(ctrl)':8}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}")
-        result += (
-            f"#{'T(ctrl)':8}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
-        )
+        print(f"#{'T(ctrl)':>8}  {'F':>20}  {'stat_err':>9}  {'inte_err':>9}  {'err':>9}")
+        result += f"#{'T(ctrl)':>8}  {'F':>20}  {'stat_err':>9}  {'inte_err':>9}  {'err':>9}\n"
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -635,9 +621,9 @@ def post_tasks(
             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"
     elif "npt" in ens:
         print(
-            f"#{'T(ctrl)':8}  {'P(ctrl)':15}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}"
+            f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>20}  {'stat_err':>9}  {'inte_err':>9}  {'err':>9}"
         )
-        result += f"#{'T(ctrl)':8}  {'P(ctrl)':15}  {'F':20}  {'stat_err':9}  {'inte_err':9}  {'err':9}\n"
+        result += f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>20}  {'stat_err':>9}  {'inte_err':>9}  {'err':>9}\n"
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -738,9 +724,7 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
             ukn = np.concatenate((ukn, block_u), axis=1)
     nk = np.array(nk)
 
-    info0 = _compute_thermo(
-        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
-    )
+    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -786,9 +770,7 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
                 f"{all_temps[ii]:9.2f}  {all_fe[ii]:20.12f}  {all_fe_err[ii]:9.2e}  {all_fe_sys_err[ii]:9.2e}"
             )
     elif "npt" in ens:
-        print(
-            f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}"
-        )
+        print(f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}")
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -810,9 +792,7 @@ def refine_task(from_task, to_task, err):
 
     from_ti = os.path.join(from_task, "ti.out")
     if not os.path.isfile(from_ti):
-        raise RuntimeError(
-            f"cannot find file {from_ti}, task should be computed befor refined"
-        )
+        raise RuntimeError(f"cannot find file {from_ti}, task should be computed befor refined")
     tmp_array = np.loadtxt(from_ti)
     all_t = tmp_array[:, 0]
     integrand = tmp_array[:, 1]
@@ -942,9 +922,7 @@ def add_module_subparsers(main_subparsers):
     )
     parser_gen.set_defaults(func=handle_gen)
 
-    parser_compute = module_subparsers.add_parser(
-        "compute", help="Compute the result of a job"
-    )
+    parser_compute = module_subparsers.add_parser("compute", help="Compute the result of a job")
     parser_compute.add_argument("JOB", type=str, help="folder of the job")
     parser_compute.add_argument(
         "-m",
@@ -983,15 +961,9 @@ def add_module_subparsers(main_subparsers):
     )
     parser_compute.set_defaults(func=handle_compute)
 
-    parser_refine = module_subparsers.add_parser(
-        "refine", help="Refine the grid of a job"
-    )
-    parser_refine.add_argument(
-        "-i", "--input", type=str, required=True, help="input job"
-    )
-    parser_refine.add_argument(
-        "-o", "--output", type=str, required=True, help="output job"
-    )
+    parser_refine = module_subparsers.add_parser("refine", help="Refine the grid of a job")
+    parser_refine.add_argument("-i", "--input", type=str, required=True, help="input job")
+    parser_refine.add_argument("-o", "--output", type=str, required=True, help="output job")
     parser_refine.add_argument(
         "-e", "--error", type=float, required=True, help="the error required"
     )
@@ -1031,9 +1003,7 @@ def handle_compute(args):
                 raise ValueError("Cannot find temperature in hti's input json file")
         elif path == "p":
             try:
-                args.To = get_first_matched_key_from_dict(
-                    jdata_hti_in, ["pres", "press"]
-                )
+                args.To = get_first_matched_key_from_dict(jdata_hti_in, ["pres", "press"])
             except KeyError:
                 args.To = None
             if args.To is None:

From 6d71f0aa3913ebcf2e69aa2bcfe5a626526d28ee Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Dec 2025 09:41:48 +0000
Subject: [PATCH 5/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dpti/ti.py | 76 +++++++++++++++++++++++++++++++++++++-----------------
 1 file changed, 53 insertions(+), 23 deletions(-)

diff --git a/dpti/ti.py b/dpti/ti.py
index 5f2b385e..18337b9e 100755
--- a/dpti/ti.py
+++ b/dpti/ti.py
@@ -118,15 +118,11 @@ def _gen_lammps_input(
     if ens == "nvt":
         ret += "fix             1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}\n"
     elif ens == "npt-iso" or ens == "npt":
-        ret += (
-            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
-        )
+        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-aniso":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-tri":
-        ret += (
-            "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
-        )
+        ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} tri ${PRES} ${PRES} ${TAU_P}\n"
     elif ens == "npt-xy":
         ret += "fix             1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P} couple xy\n"
     elif ens == "nve":
@@ -165,7 +161,9 @@ def make_tasks(iter_name, jdata, if_meam=None):
     timestep = get_first_matched_key_from_dict(jdata, ["timestep", "dt"])
     # thermo_freq = jdata['thermo_freq']
     thermo_freq = get_first_matched_key_from_dict(jdata, ["thermo_freq", "stat_freq"])
-    dump_freq = get_first_matched_key_from_dict(jdata, ["dump_freq", "thermo_freq", "stat_freq"])
+    dump_freq = get_first_matched_key_from_dict(
+        jdata, ["dump_freq", "thermo_freq", "stat_freq"]
+    )
     # thermos = jdata['thermos']
     ens = jdata["ens"]
     path = jdata["path"]
@@ -373,7 +371,9 @@ def _print_thermo_info(info, more_head=""):
     print(ptr)
 
 
-def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None):
+def _thermo_inte(
+    jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s", all_e=None
+):
     path = jdata["path"]
     ens = jdata["ens"]
     all_temps = []
@@ -408,7 +408,9 @@ def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s",
 
     #     return np.asarray(all_temps), np.asarray(all_press), np.asarray(all_fe), np.asarray(all_fe_err), np.asarray(all_fe_sys_err)
 
-    all_t, inte, inte_e, stat_e = integrate_range(all_t, integrand, integrand_err, scheme)
+    all_t, inte, inte_e, stat_e = integrate_range(
+        all_t, integrand, integrand_err, scheme
+    )
     for ii in range(0, len(all_t)):
         diff_e = inte[ii]
         err = stat_e[ii]
@@ -422,7 +424,9 @@ def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s",
             sys_err *= all_t[ii]
             all_temps.append(all_t[ii])
             if "npt" in ens:
-                all_press.append(get_first_matched_key_from_dict(jdata, ["pres", "press"]))
+                all_press.append(
+                    get_first_matched_key_from_dict(jdata, ["pres", "press"])
+                )
         elif path == "p":
             e1 = Eo + diff_e
             err = np.sqrt(np.square(Eo_err) + np.square(err))
@@ -440,7 +444,9 @@ def _thermo_inte(jdata, Eo, Eo_err, all_t, integrand, integrand_err, scheme="s",
     )
 
 
-def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0):
+def post_tasks(
+    iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="simpson", shift=0.0
+):
     equi_conf = get_task_file_abspath(iter_name, jdata["equi_conf"])
     if natoms is None:
         natoms = get_natoms(equi_conf)
@@ -549,7 +555,9 @@ def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="sim
         header="t/p Integrand U/V U/V_err enthalpy msd_xyz",
     )
 
-    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
+    info0 = _compute_thermo(
+        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
+    )
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -578,14 +586,18 @@ def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="sim
             all_fe_1,
             all_fe_err_1,
             all_fe_sys_err_1,
-        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme)
+        ) = _thermo_inte(
+            jdata, Eo, Eo_err, all_t_1, integrand_1, integrand_err_1, scheme=scheme
+        )
         (
             all_temps_2,
             all_press_2,
             all_fe_2,
             all_fe_err_2,
             all_fe_sys_err_2,
-        ) = _thermo_inte(jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme)
+        ) = _thermo_inte(
+            jdata, Eo, Eo_err, all_t_2, integrand_2, integrand_err_2, scheme=scheme
+        )
         all_temps_1 = np.flip(all_temps_1, 0)
         all_press_1 = np.flip(all_press_1, 0)
         all_fe_1 = np.flip(all_fe_1, 0)
@@ -612,7 +624,9 @@ def post_tasks(iter_name, jdata, Eo, Eo_err=0, To=None, natoms=None, scheme="sim
     result = ""
     # result_file = open(f"{iter_name}/../result", 'w')
     if "nvt" == ens:
-        print(f"#{'T(ctrl)':>8}  {'F':>20}  {'stat_err':>9}  {'inte_err':>9}  {'err':>9}")
+        print(
+            f"#{'T(ctrl)':>8}  {'F':>20}  {'stat_err':>9}  {'inte_err':>9}  {'err':>9}"
+        )
         result += f"#{'T(ctrl)':>8}  {'F':>20}  {'stat_err':>9}  {'inte_err':>9}  {'err':>9}\n"
         for ii in range(len(all_temps)):
             print(
@@ -724,7 +738,9 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
             ukn = np.concatenate((ukn, block_u), axis=1)
     nk = np.array(nk)
 
-    info0 = _compute_thermo(os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize)
+    info0 = _compute_thermo(
+        os.path.join(all_tasks[0], "log.lammps"), natoms, stat_skip, stat_bsize
+    )
     info1 = _compute_thermo(
         os.path.join(all_tasks[-1], "log.lammps"), natoms, stat_skip, stat_bsize
     )
@@ -770,7 +786,9 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
                 f"{all_temps[ii]:9.2f}  {all_fe[ii]:20.12f}  {all_fe_err[ii]:9.2e}  {all_fe_sys_err[ii]:9.2e}"
             )
     elif "npt" in ens:
-        print(f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}")
+        print(
+            f"#{'T(ctrl)':>8}  {'P(ctrl)':>15}  {'F':>15}  {'stat_err':>9}  {'inte_err':>9}"
+        )
         for ii in range(len(all_temps)):
             print(
                 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}"
@@ -792,7 +810,9 @@ def refine_task(from_task, to_task, err):
 
     from_ti = os.path.join(from_task, "ti.out")
     if not os.path.isfile(from_ti):
-        raise RuntimeError(f"cannot find file {from_ti}, task should be computed befor refined")
+        raise RuntimeError(
+            f"cannot find file {from_ti}, task should be computed befor refined"
+        )
     tmp_array = np.loadtxt(from_ti)
     all_t = tmp_array[:, 0]
     integrand = tmp_array[:, 1]
@@ -922,7 +942,9 @@ def add_module_subparsers(main_subparsers):
     )
     parser_gen.set_defaults(func=handle_gen)
 
-    parser_compute = module_subparsers.add_parser("compute", help="Compute the result of a job")
+    parser_compute = module_subparsers.add_parser(
+        "compute", help="Compute the result of a job"
+    )
     parser_compute.add_argument("JOB", type=str, help="folder of the job")
     parser_compute.add_argument(
         "-m",
@@ -961,9 +983,15 @@ def add_module_subparsers(main_subparsers):
     )
     parser_compute.set_defaults(func=handle_compute)
 
-    parser_refine = module_subparsers.add_parser("refine", help="Refine the grid of a job")
-    parser_refine.add_argument("-i", "--input", type=str, required=True, help="input job")
-    parser_refine.add_argument("-o", "--output", type=str, required=True, help="output job")
+    parser_refine = module_subparsers.add_parser(
+        "refine", help="Refine the grid of a job"
+    )
+    parser_refine.add_argument(
+        "-i", "--input", type=str, required=True, help="input job"
+    )
+    parser_refine.add_argument(
+        "-o", "--output", type=str, required=True, help="output job"
+    )
     parser_refine.add_argument(
         "-e", "--error", type=float, required=True, help="the error required"
     )
@@ -1003,7 +1031,9 @@ def handle_compute(args):
                 raise ValueError("Cannot find temperature in hti's input json file")
         elif path == "p":
             try:
-                args.To = get_first_matched_key_from_dict(jdata_hti_in, ["pres", "press"])
+                args.To = get_first_matched_key_from_dict(
+                    jdata_hti_in, ["pres", "press"]
+                )
             except KeyError:
                 args.To = None
             if args.To is None:

From 7bb4d6df4d366cffeadbc9657d14700a0eb37887 Mon Sep 17 00:00:00 2001
From: "C. Thang Nguyen" <thangckt@gmail.com>
Date: Thu, 11 Dec 2025 22:18:35 +0900
Subject: [PATCH 6/9] Refactor string formatting and fix typo in dpti modules

Updated dpti/relax.py to use f-strings for variable assignments and mass mapping for improved readability. Removed unused ntasks variable in dpti/ti.py and fixed a typo in an error message ('befor' to 'before').
---
 dpti/relax.py | 6 +++---
 dpti/ti.py    | 4 +---
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/dpti/relax.py b/dpti/relax.py
index ec01c8bf..2a89a734 100755
--- a/dpti/relax.py
+++ b/dpti/relax.py
@@ -12,8 +12,8 @@ def _gen_lammps_relax(conf_file, mass_map, model, pres, thermo_freq=100, dump_fr
     ret = ""
     ret += "clear\n"
     ret += "# --------------------- VARIABLES-------------------------\n"
-    ret += "variable        THERMO_FREQ     equal %d\n" % thermo_freq
-    ret += "variable        DUMP_FREQ       equal %d\n" % dump_freq
+    ret += f"variable        THERMO_FREQ     equal {thermo_freq}\n"
+    ret += f"variable        DUMP_FREQ       equal {dump_freq}\n"
     ret += f"variable        PRES            equal {pres:f}\n"
     ret += "# ---------------------- INITIALIZAITION ------------------\n"
     ret += "units           metal\n"
@@ -24,7 +24,7 @@ def _gen_lammps_relax(conf_file, mass_map, model, pres, thermo_freq=100, dump_fr
     ret += f"read_data       {conf_file}\n"
     ret += "change_box      all triclinic\n"
     for jj in range(len(mass_map)):
-        ret += "mass            %d %f\n" % (jj + 1, mass_map[jj])
+        ret += f"mass            {jj + 1} {mass_map[jj]:f}\n"
     ret += "# --------------------- FORCE FIELDS ---------------------\n"
     ret += f"pair_style      deepmd {model}\n"
     ret += "pair_coeff * *\n"
diff --git a/dpti/ti.py b/dpti/ti.py
index 18337b9e..cd8e19ba 100755
--- a/dpti/ti.py
+++ b/dpti/ti.py
@@ -463,7 +463,6 @@ def post_tasks(
 
     all_tasks = glob.glob(os.path.join(iter_name, "task.[0-9]*"))
     all_tasks.sort()
-    ntasks = len(all_tasks)
 
     all_t = []
     all_e = []
@@ -680,7 +679,6 @@ def post_tasks_mbar(iter_name, jdata, Eo, natoms=None):
 
     all_tasks = glob.glob(os.path.join(iter_name, "task.[0-9]*"))
     all_tasks.sort()
-    ntasks = len(all_tasks)
 
     if "nvt" in ens and path == "t":
         # TotEng
@@ -811,7 +809,7 @@ def refine_task(from_task, to_task, err):
     from_ti = os.path.join(from_task, "ti.out")
     if not os.path.isfile(from_ti):
         raise RuntimeError(
-            f"cannot find file {from_ti}, task should be computed befor refined"
+            f"cannot find file {from_ti}, task should be computed before refined"
         )
     tmp_array = np.loadtxt(from_ti)
     all_t = tmp_array[:, 0]

From 638215ab2f9b106f26e585493654bee031bb0881 Mon Sep 17 00:00:00 2001
From: "C. Thang Nguyen" <thangckt@gmail.com>
Date: Thu, 11 Dec 2025 23:53:10 +0900
Subject: [PATCH 7/9] Update mti.py

---
 dpti/mti.py | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/dpti/mti.py b/dpti/mti.py
index 7570a2b4..cb506d14 100644
--- a/dpti/mti.py
+++ b/dpti/mti.py
@@ -50,10 +50,10 @@ def _gen_lammps_input(
     ret = ""
     ret += "clear\n"
     ret += "# --------------------- VARIABLES-------------------------\n"
-    ret += "variable        ibead           uloop %d pad\n" % (power - 1)
-    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 += f"variable        ibead           uloop {power - 1} pad\n"
+    ret += f"variable        NSTEPS          equal {nsteps:d}\n"
+    ret += f"variable        THERMO_FREQ     equal {thermo_freq:d}\n"
+    ret += f"variable        DUMP_FREQ       equal {dump_freq:d}\n"
     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"
@@ -67,9 +67,9 @@ def _gen_lammps_input(
     ret += "box             tilt large\n"
     ret += f'if "${{restart}} > 0" then "read_restart ${{ibead}}.restart.*" else "read_data {conf_file}"\n'
     if copies is not None:
-        ret += "replicate       %d %d %d\n" % (copies[0], copies[1], copies[2])
+        ret += f"replicate       {copies[0]} {copies[1]} {copies[2]}\n"
     for jj in range(len(mass_map)):
-        ret += "mass            %d %f\n" % (jj + 1, mass_map[jj] * mass_scale)
+        ret += f"mass            {jj + 1} {mass_map[jj] * mass_scale:f}\n"
     ret += "# --------------------- FORCE FIELDS ---------------------\n"
     if model is not None:
         ret += f"pair_style      deepmd {model}\n"
@@ -165,9 +165,9 @@ def make_tasks(iter_name, jdata):
         raise RuntimeError("invalid ens")
 
     job_type = jdata["job_type"]
-    assert (
-        job_type == "nbead_convergence" or job_type == "mass_ti"
-    ), "Unknow job_type. Only nbead_convergence and mass_ti are supported."
+    assert job_type == "nbead_convergence" or job_type == "mass_ti", (
+        "Unknow job_type. Only nbead_convergence and mass_ti are supported."
+    )
     mass_scale_y_seq = get_first_matched_key_from_dict(jdata, ["mass_scale_y"])
     mass_scale_y_list = parse_seq(mass_scale_y_seq)
     mass_scales = (1.0 / np.array(mass_scale_y_list)) ** 2
@@ -176,13 +176,13 @@ def make_tasks(iter_name, jdata):
     nnode_seq = jdata.get("nnode", None)
     if nnode_seq is not None:
         nnode_list = parse_seq(nnode_seq)
-        assert (
-            len(nbead_list) == len(nnode_list)
-        ), "Lists nbead and nnode should have same length. Please specify one nnode for each nbead."
+        assert len(nbead_list) == len(nnode_list), (
+            "Lists nbead and nnode should have same length. Please specify one nnode for each nbead."
+        )
     if job_type == "mass_ti":
-        assert (
-            len(mass_scale_y_list) == len(nbead_list)
-        ), "For mass TI tasks, you must provide one value of nbead for each value of mass_scale_y."
+        assert len(mass_scale_y_list) == len(nbead_list), (
+            "For mass TI tasks, you must provide one value of nbead for each value of mass_scale_y."
+        )
 
     job_abs_dir = create_path(iter_name)
     ti_settings["equi_conf"] = relative_link_file(equi_conf, job_abs_dir)
@@ -194,7 +194,7 @@ def make_tasks(iter_name, jdata):
         json.dump(ti_settings, f, indent=4)
 
     for ii in range(ntasks):
-        task_dir = os.path.join(job_abs_dir, "task.%06d" % ii)
+        task_dir = os.path.join(job_abs_dir, f"task.{ii:06d}")
         task_abs_dir = create_path(task_dir)
         settings = {}
         if path == "t":
@@ -207,12 +207,12 @@ def make_tasks(iter_name, jdata):
         settings["pres"] = pres
         if job_type == "nbead_convergence":
             for jj in range(len(mass_scale_y_list)):
-                mass_scale_y_dir = os.path.join(task_abs_dir, "mass_scale_y.%06d" % jj)
+                mass_scale_y_dir = os.path.join(task_abs_dir, f"mass_scale_y.{jj:06d}")
                 mass_scale_y_abs_dir = create_path(mass_scale_y_dir)
                 settings["mass_scale_y"] = mass_scale_y_list[jj]
                 settings["mass_scale"] = mass_scales[jj]
                 for kk in range(len(nbead_list)):
-                    nbead_dir = os.path.join(mass_scale_y_abs_dir, "nbead.%06d" % kk)
+                    nbead_dir = os.path.join(mass_scale_y_abs_dir, f"nbead.{kk:06d}")
                     nbead_abs_dir = create_path(nbead_dir)
                     settings["nbead"] = nbead_list[kk]
                     if nnode_seq is not None:
@@ -263,7 +263,7 @@ def make_tasks(iter_name, jdata):
                         json.dump(settings, f, indent=4)
         elif job_type == "mass_ti":
             for jj in range(len(mass_scale_y_list)):
-                mass_scale_y_dir = os.path.join(task_abs_dir, "mass_scale_y.%06d" % jj)
+                mass_scale_y_dir = os.path.join(task_abs_dir, f"mass_scale_y.{jj:06d}")
                 mass_scale_y_abs_dir = create_path(mass_scale_y_dir)
                 settings["mass_scale_y"] = mass_scale_y_list[jj]
                 settings["mass_scale"] = mass_scales[jj]

From 198b518e1a03305feed03b7a745acbcbefcc48b8 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Dec 2025 14:53:23 +0000
Subject: [PATCH 8/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dpti/mti.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/dpti/mti.py b/dpti/mti.py
index cb506d14..659b1f8d 100644
--- a/dpti/mti.py
+++ b/dpti/mti.py
@@ -165,9 +165,9 @@ def make_tasks(iter_name, jdata):
         raise RuntimeError("invalid ens")
 
     job_type = jdata["job_type"]
-    assert job_type == "nbead_convergence" or job_type == "mass_ti", (
-        "Unknow job_type. Only nbead_convergence and mass_ti are supported."
-    )
+    assert (
+        job_type == "nbead_convergence" or job_type == "mass_ti"
+    ), "Unknow job_type. Only nbead_convergence and mass_ti are supported."
     mass_scale_y_seq = get_first_matched_key_from_dict(jdata, ["mass_scale_y"])
     mass_scale_y_list = parse_seq(mass_scale_y_seq)
     mass_scales = (1.0 / np.array(mass_scale_y_list)) ** 2
@@ -176,13 +176,13 @@ def make_tasks(iter_name, jdata):
     nnode_seq = jdata.get("nnode", None)
     if nnode_seq is not None:
         nnode_list = parse_seq(nnode_seq)
-        assert len(nbead_list) == len(nnode_list), (
-            "Lists nbead and nnode should have same length. Please specify one nnode for each nbead."
-        )
+        assert (
+            len(nbead_list) == len(nnode_list)
+        ), "Lists nbead and nnode should have same length. Please specify one nnode for each nbead."
     if job_type == "mass_ti":
-        assert len(mass_scale_y_list) == len(nbead_list), (
-            "For mass TI tasks, you must provide one value of nbead for each value of mass_scale_y."
-        )
+        assert (
+            len(mass_scale_y_list) == len(nbead_list)
+        ), "For mass TI tasks, you must provide one value of nbead for each value of mass_scale_y."
 
     job_abs_dir = create_path(iter_name)
     ti_settings["equi_conf"] = relative_link_file(equi_conf, job_abs_dir)

From 786cda3f26cc8b8520ea8b7b9b3bc78ef58c0c60 Mon Sep 17 00:00:00 2001
From: "C. Thang Nguyen" <thangckt@gmail.com>
Date: Thu, 11 Dec 2025 23:57:49 +0900
Subject: [PATCH 9/9] Update mti.py

---
 dpti/mti.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dpti/mti.py b/dpti/mti.py
index cb506d14..4f604819 100644
--- a/dpti/mti.py
+++ b/dpti/mti.py
@@ -50,7 +50,7 @@ def _gen_lammps_input(
     ret = ""
     ret += "clear\n"
     ret += "# --------------------- VARIABLES-------------------------\n"
-    ret += f"variable        ibead           uloop {power - 1} pad\n"
+    ret += f"variable        ibead           uloop {(power - 1):d} pad\n"
     ret += f"variable        NSTEPS          equal {nsteps:d}\n"
     ret += f"variable        THERMO_FREQ     equal {thermo_freq:d}\n"
     ret += f"variable        DUMP_FREQ       equal {dump_freq:d}\n"
@@ -69,7 +69,7 @@ def _gen_lammps_input(
     if copies is not None:
         ret += f"replicate       {copies[0]} {copies[1]} {copies[2]}\n"
     for jj in range(len(mass_map)):
-        ret += f"mass            {jj + 1} {mass_map[jj] * mass_scale:f}\n"
+        ret += f"mass            {jj + 1} {(mass_map[jj] * mass_scale):f}\n"
     ret += "# --------------------- FORCE FIELDS ---------------------\n"
     if model is not None:
         ret += f"pair_style      deepmd {model}\n"