pymdkit 1.5.3__tar.gz → 1.5.4__tar.gz

{pymdkit-1.5.3 → pymdkit-1.5.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.5.3
+Version: 1.5.4
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -136,7 +136,7 @@ pmk submit-vasp -subscript sub_vasp -queue slurm -max-job-num 30
 nohup pmk submit-vasp -subscript sub_vasp -queue slurm -max-job-num 30 > submit-vasp.log 2>&1 &
 pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6
 pmk realloc-occ -if cifs -of chg-balance -formula Li3YCl6
-pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6 -occ 0 0.25 0.5 0.75 1
+pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6 -occ 0 0.125 0.25 0.375 0.5 0.625 0.75 0.875 1
 pmk substitute -i Li3YCl6.cif -se Li -sn 3 -we Na -wn 3 -on 100
 pmk substitute -i Li3YCl6.cif -se Li -sn 3 -we none -on 100
 pmk substitute -i Li96Ta6La11Cl72.cif -se Li1 Li2 -sn 20 67 -we none -on 100
@@ -214,8 +214,9 @@ the last 50% of the SDC correlation-time range, converts A^2/ps to cm^2/s by
 multiplying by `1e-4`, and reports `D_total = (D_x + D_y + D_z) / 3`.
 Each job receives `msd/group_INDEX_ELEMENT_TEMP_msd.txt`, a matching `_sdc.txt`,
 and a `_results.txt`. The root receives a compact `sigma-sdc-summary.txt` with
-one row per job folder. Conductivities use two decimal places; diffusion
-coefficients use compact scientific notation with two decimal places. If the
+one fixed-width, right-aligned row per job folder. Conductivities use two
+decimal places; diffusion coefficients use compact scientific notation with
+two decimal places. If the
 mobile ion occupies multiple groups, conductivities are summed and diffusion
 coefficients are particle-count-weighted.
 
@@ -237,8 +238,8 @@ Wyckoff labels, and CIF layout. Every input receives `OUTPUT/INPUT_STEM/`; for
 the supplied Li4YCl6 example, the two outputs are `...-d1.cif` with `Li1=0.50`
 and `...-d2.cif` with `Li2=0.50`. Folder mode uses `-if` with the same `-of` and
 `-formula` options. Add `-occ` followed by the only permitted occupancy values;
-for example, `-occ 0 0.25 0.5 0.75 1` also permits the valid allocation
-`Li1=0.75, Li2=0.75`.
+three decimal places are supported, so grids containing `0.125`, `0.375`,
+`0.625`, and `0.875` are preserved exactly in generated CIF files.
 
 `gather-fs` recursively scans all job folders below the current directory. For
 VASP it follows the global `vaspout.h5 > vasprun.xml > OUTCAR` priority and
@@ -305,7 +306,7 @@ and `Cl`. Oxidation numbers remain in the separate
 
 Newly serialized floating-point values use eight digits after the decimal
 point across PMK structure, trajectory, data, report, and screen output. CIF
-`_atom_site_occupancy` values use two digits and
+`_atom_site_occupancy` values use three digits and
 `_atom_type_oxidation_number` values use one digit. In extended XYZ, zero components
 inside the second-line `Lattice="..."` value remain `0.0`; other generated
 floating-point values use eight digits. Commands that select or concatenate

{pymdkit-1.5.3 → pymdkit-1.5.4}/README.md

@@ -109,7 +109,7 @@ pmk submit-vasp -subscript sub_vasp -queue slurm -max-job-num 30
 nohup pmk submit-vasp -subscript sub_vasp -queue slurm -max-job-num 30 > submit-vasp.log 2>&1 &
 pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6
 pmk realloc-occ -if cifs -of chg-balance -formula Li3YCl6
-pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6 -occ 0 0.25 0.5 0.75 1
+pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6 -occ 0 0.125 0.25 0.375 0.5 0.625 0.75 0.875 1
 pmk substitute -i Li3YCl6.cif -se Li -sn 3 -we Na -wn 3 -on 100
 pmk substitute -i Li3YCl6.cif -se Li -sn 3 -we none -on 100
 pmk substitute -i Li96Ta6La11Cl72.cif -se Li1 Li2 -sn 20 67 -we none -on 100
@@ -187,8 +187,9 @@ the last 50% of the SDC correlation-time range, converts A^2/ps to cm^2/s by
 multiplying by `1e-4`, and reports `D_total = (D_x + D_y + D_z) / 3`.
 Each job receives `msd/group_INDEX_ELEMENT_TEMP_msd.txt`, a matching `_sdc.txt`,
 and a `_results.txt`. The root receives a compact `sigma-sdc-summary.txt` with
-one row per job folder. Conductivities use two decimal places; diffusion
-coefficients use compact scientific notation with two decimal places. If the
+one fixed-width, right-aligned row per job folder. Conductivities use two
+decimal places; diffusion coefficients use compact scientific notation with
+two decimal places. If the
 mobile ion occupies multiple groups, conductivities are summed and diffusion
 coefficients are particle-count-weighted.
 
@@ -210,8 +211,8 @@ Wyckoff labels, and CIF layout. Every input receives `OUTPUT/INPUT_STEM/`; for
 the supplied Li4YCl6 example, the two outputs are `...-d1.cif` with `Li1=0.50`
 and `...-d2.cif` with `Li2=0.50`. Folder mode uses `-if` with the same `-of` and
 `-formula` options. Add `-occ` followed by the only permitted occupancy values;
-for example, `-occ 0 0.25 0.5 0.75 1` also permits the valid allocation
-`Li1=0.75, Li2=0.75`.
+three decimal places are supported, so grids containing `0.125`, `0.375`,
+`0.625`, and `0.875` are preserved exactly in generated CIF files.
 
 `gather-fs` recursively scans all job folders below the current directory. For
 VASP it follows the global `vaspout.h5 > vasprun.xml > OUTCAR` priority and
@@ -278,7 +279,7 @@ and `Cl`. Oxidation numbers remain in the separate
 
 Newly serialized floating-point values use eight digits after the decimal
 point across PMK structure, trajectory, data, report, and screen output. CIF
-`_atom_site_occupancy` values use two digits and
+`_atom_site_occupancy` values use three digits and
 `_atom_type_oxidation_number` values use one digit. In extended XYZ, zero components
 inside the second-line `Lattice="..."` value remain `0.0`; other generated
 floating-point values use eight digits. Commands that select or concatenate

{pymdkit-1.5.3 → pymdkit-1.5.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.5.3"
+version = "1.5.4"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.5.3 → pymdkit-1.5.4}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.5.3"
+__version__ = "1.5.4"

{pymdkit-1.5.3 → pymdkit-1.5.4}/src/pymdkit/commands/_cifio.py

@@ -198,7 +198,7 @@ def _format_cif_scalar(value, precision, force=False):
 def _format_cif_numbers(block):
     for tag, value in list(block.data.items()):
         if tag == OCCUPANCY_TAG:
-            precision = 2
+            precision = 3
         elif tag == OXIDATION_TAG:
             precision = 1
         else:

{pymdkit-1.5.3 → pymdkit-1.5.4}/src/pymdkit/commands/gpumd_msd.py

@@ -402,13 +402,7 @@ def write_summary(root, records, diffuse_ion):
         "sigma_y(mS/cm)", "sigma_z(mS/cm)", "D_total(cm^2/s)",
         "D_x(cm^2/s)", "D_y(cm^2/s)", "D_z(cm^2/s)",
     ]
-    lines = [
-        "GPUMD SDC and Nernst-Einstein conductivity summary",
-        f"Mobile ion: {diffuse_ion}",
-        "SDC average: arithmetic mean over the last 50% of correlation time",
-        "\t".join(columns),
-        "-" * len("\t".join(columns).expandtabs(4)),
-    ]
+    rows = []
     jobs = {}
     for record in records:
         if record["element"] == diffuse_ion and record["conductivity"] is not None:
@@ -425,7 +419,31 @@ def write_summary(root, records, diffuse_ion):
             *(_compact_scientific(diffusion[index])
               for index in (3, 0, 1, 2)),
         ]
-        lines.append("\t".join(fields))
+        rows.append(fields)
+    widths = [
+        max(len(columns[index]), *(len(row[index]) for row in rows))
+        for index in range(len(columns))
+    ]
+    header = "  ".join(
+        f"{column:<{widths[index]}}" if index == 0
+        else f"{column:>{widths[index]}}"
+        for index, column in enumerate(columns)
+    )
+    lines = [
+        "GPUMD SDC and Nernst-Einstein conductivity summary",
+        f"Mobile ion: {diffuse_ion}",
+        "SDC average: arithmetic mean over the last 50% of correlation time",
+        header,
+        "-" * len(header),
+    ]
+    lines.extend(
+        "  ".join(
+            f"{value:<{widths[index]}}" if index == 0
+            else f"{value:>{widths[index]}}"
+            for index, value in enumerate(row)
+        )
+        for row in rows
+    )
     (Path(root) / SUMMARY_FILE).write_text(
         "\n".join(lines) + "\n", encoding="utf-8")
 

{pymdkit-1.5.3 → pymdkit-1.5.4}/src/pymdkit/commands/realloc_occ.py

@@ -253,9 +253,9 @@ def _normalize_occupancies(values):
         number = float(value)
         if not -TOLERANCE <= number <= 1.0 + TOLERANCE:
             raise ValueError("-occ values must be between 0 and 1")
-        rounded = round(number, 2)
+        rounded = round(number, 3)
         if abs(number - rounded) > TOLERANCE:
-            raise ValueError("-occ values support at most two decimal places")
+            raise ValueError("-occ values support at most three decimal places")
         occupancies.append(min(1.0, max(0.0, rounded)))
     result = tuple(sorted(set(occupancies)))
     if not result:
@@ -302,7 +302,7 @@ def _grid_occupancy_options(sites, target_count, allowed_occupancies):
         values,
     ))
     if not options:
-        allowed = ", ".join(f"{value:.2f}" for value in allowed_occupancies)
+        allowed = ", ".join(f"{value:.3f}" for value in allowed_occupancies)
         raise ValueError(
             f"no allocation reaches the target using -occ values: {allowed}"
         )
@@ -350,7 +350,7 @@ def _adjustment_options(sites, target_count, allowed_occupancies=None):
         for site, amount in zip(sites, adjustment):
             change = amount / site.multiplicity
             value = site.occupancy + change if increase else site.occupancy - change
-            values.append(round(min(1.0, max(0.0, value)), 2))
+            values.append(round(min(1.0, max(0.0, value)), 3))
         if abs(sum(site.multiplicity * value
                    for site, value in zip(sites, values)) - target_count) <= TOLERANCE:
             options.append(tuple(values))
@@ -428,7 +428,7 @@ def render_candidate(parsed, occupancies, target, target_counts, z, output):
     occupancy_index = site_loop.headers.index("_atom_site_occupancy")
     for site, occupancy in zip(parsed.sites, occupancies):
         tokens = list(site.row.tokens)
-        tokens[occupancy_index] = f"{occupancy:.2f}"
+        tokens[occupancy_index] = f"{occupancy:.3f}"
         lines[site.row.line_index] = "  " + "  ".join(tokens)
 
     output = Path(output)
@@ -475,7 +475,7 @@ def process_one(source, output_root, target_formula, allowed_occupancies=None):
     for number, (occupancies, charge) in enumerate(candidates, start=1):
         output = destination / f"{Path(source).stem}-d{number}.cif"
         render_candidate(parsed, occupancies, target, target_counts, z, output)
-        changes = [f"{site.label}={occupancy:.2f}"
+        changes = [f"{site.label}={occupancy:.3f}"
                    for site, occupancy in zip(parsed.sites, occupancies)
                    if abs(site.occupancy - occupancy) > TOLERANCE]
         print(f"  {output.name}: {', '.join(changes)}; charge={charge:.8f}")
@@ -491,7 +491,7 @@ def add_arguments(parser):
                         help="Target reduced formula, for example Li3YCl6.")
     parser.add_argument(
         "-occ", nargs="+", type=float,
-        help="Allowed site occupancies, for example 0 0.25 0.5 0.75 1.",
+        help="Allowed site occupancies, for example 0 0.125 0.25 ... 0.875 1.",
     )
 
 

{pymdkit-1.5.3 → pymdkit-1.5.4}/src/pymdkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.5.3
+Version: 1.5.4
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -136,7 +136,7 @@ pmk submit-vasp -subscript sub_vasp -queue slurm -max-job-num 30
 nohup pmk submit-vasp -subscript sub_vasp -queue slurm -max-job-num 30 > submit-vasp.log 2>&1 &
 pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6
 pmk realloc-occ -if cifs -of chg-balance -formula Li3YCl6
-pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6 -occ 0 0.25 0.5 0.75 1
+pmk realloc-occ -i 66-Li4YCl6-5.cif -of chg-balance -formula Li3YCl6 -occ 0 0.125 0.25 0.375 0.5 0.625 0.75 0.875 1
 pmk substitute -i Li3YCl6.cif -se Li -sn 3 -we Na -wn 3 -on 100
 pmk substitute -i Li3YCl6.cif -se Li -sn 3 -we none -on 100
 pmk substitute -i Li96Ta6La11Cl72.cif -se Li1 Li2 -sn 20 67 -we none -on 100
@@ -214,8 +214,9 @@ the last 50% of the SDC correlation-time range, converts A^2/ps to cm^2/s by
 multiplying by `1e-4`, and reports `D_total = (D_x + D_y + D_z) / 3`.
 Each job receives `msd/group_INDEX_ELEMENT_TEMP_msd.txt`, a matching `_sdc.txt`,
 and a `_results.txt`. The root receives a compact `sigma-sdc-summary.txt` with
-one row per job folder. Conductivities use two decimal places; diffusion
-coefficients use compact scientific notation with two decimal places. If the
+one fixed-width, right-aligned row per job folder. Conductivities use two
+decimal places; diffusion coefficients use compact scientific notation with
+two decimal places. If the
 mobile ion occupies multiple groups, conductivities are summed and diffusion
 coefficients are particle-count-weighted.
 
@@ -237,8 +238,8 @@ Wyckoff labels, and CIF layout. Every input receives `OUTPUT/INPUT_STEM/`; for
 the supplied Li4YCl6 example, the two outputs are `...-d1.cif` with `Li1=0.50`
 and `...-d2.cif` with `Li2=0.50`. Folder mode uses `-if` with the same `-of` and
 `-formula` options. Add `-occ` followed by the only permitted occupancy values;
-for example, `-occ 0 0.25 0.5 0.75 1` also permits the valid allocation
-`Li1=0.75, Li2=0.75`.
+three decimal places are supported, so grids containing `0.125`, `0.375`,
+`0.625`, and `0.875` are preserved exactly in generated CIF files.
 
 `gather-fs` recursively scans all job folders below the current directory. For
 VASP it follows the global `vaspout.h5 > vasprun.xml > OUTCAR` priority and
@@ -305,7 +306,7 @@ and `Cl`. Oxidation numbers remain in the separate
 
 Newly serialized floating-point values use eight digits after the decimal
 point across PMK structure, trajectory, data, report, and screen output. CIF
-`_atom_site_occupancy` values use two digits and
+`_atom_site_occupancy` values use three digits and
 `_atom_type_oxidation_number` values use one digit. In extended XYZ, zero components
 inside the second-line `Lattice="..."` value remain `0.0`; other generated
 floating-point values use eight digits. Commands that select or concatenate