mdkits 1.0.5__tar.gz → 1.0.7__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (48) hide show
  1. {mdkits-1.0.5 → mdkits-1.0.7}/PKG-INFO +1 -1
  2. {mdkits-1.0.5 → mdkits-1.0.7}/pyproject.toml +1 -1
  3. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/density.py +2 -2
  4. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/msd.py +1 -1
  5. {mdkits-1.0.5 → mdkits-1.0.7}/LICENSE +0 -0
  6. {mdkits-1.0.5 → mdkits-1.0.7}/README.md +0 -0
  7. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/__init__.py +0 -0
  8. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/__init__.py +0 -0
  9. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/adsorbate.py +0 -0
  10. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/build_bulk.py +0 -0
  11. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/build_cli.py +0 -0
  12. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/build_interface.py +0 -0
  13. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/build_solution.py +0 -0
  14. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/build_surface.py +0 -0
  15. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/cut_surface.py +0 -0
  16. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/supercell.py +0 -0
  17. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/build_cli/water.xyz +0 -0
  18. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/convert.py +0 -0
  19. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/data.py +0 -0
  20. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/extract.py +0 -0
  21. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/plot.py +0 -0
  22. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/config/__init__.py +0 -0
  23. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/config/settings.yml +0 -0
  24. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/dft_cli/check_neb.py +0 -0
  25. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/dft_cli/cube.py +0 -0
  26. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/dft_cli/dft_cli.py +0 -0
  27. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/dft_cli/pdos.py +0 -0
  28. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/angle.py +0 -0
  29. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/dipole.py +0 -0
  30. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/hb_distribution.py +0 -0
  31. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/md_cli.py +0 -0
  32. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/monitor.py +0 -0
  33. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/rdf.py +0 -0
  34. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/setting.py +0 -0
  35. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/vac.py +0 -0
  36. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/wrap.py +0 -0
  37. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/mdkits.py +0 -0
  38. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/.fig_operation.py.swp +0 -0
  39. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/__init__.py +0 -0
  40. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/arg_type.py +0 -0
  41. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/cp2k_input_parsing.py +0 -0
  42. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/encapsulated_ase.py +0 -0
  43. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/encapsulated_mda.py +0 -0
  44. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/fig_operation.py +0 -0
  45. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/numpy_geo.py +0 -0
  46. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/os_operation.py +0 -0
  47. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/out_err.py +0 -0
  48. {mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/util/structure_parsing.py +0 -0
{mdkits-1.0.5 → mdkits-1.0.7}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: mdkits
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- Version: 1.0.5
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+ Version: 1.0.7
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  Summary: kits for md or dft
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  License: MIT
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  Keywords: molecular dynamics,density functional theory
{mdkits-1.0.5 → mdkits-1.0.7}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "mdkits"
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- version = "1.0.5"
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+ version = "1.0.7"
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  description = "kits for md or dft"
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  readme = "README.md"
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  authors = ["jxxcr <jixxcr@qq.com>"]
{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/density.py RENAMED
@@ -1,7 +1,7 @@
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  #!/usr/bin/env python3
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  import numpy as np
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- import click
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+ import click, math
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  from MDAnalysis import Universe
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  from MDAnalysis.analysis.base import AnalysisBase
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  from mdkits.util import (
@@ -88,7 +88,7 @@ class Density_distribution(AnalysisBase):
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  def _conclude(self):
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  if self.frame_count > 0:
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- V = self.u.dimensions[0] * self.u.dimensions[1] * self.bin_size
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+ V = self.u.dimensions[0] * self.u.dimensions[1] * math.sin(math.radians(180 - self.u.dimensions[-1])) * self.bin_size
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  if self.atomic_mass:
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  density_distribution = (self.density_distribution * self.atomic_mass * 1.660539 / V) / self.frame_count
{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/msd.py RENAMED
@@ -16,8 +16,8 @@ def main(filename, type, group):
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  data = np.arange(1, MSD.n_frames + 1).reshape(-1, 1)
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  s = "_"
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- o = f"msd_{type}_{'_'.join(group).replace(' ', '_')}.dat"
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  name = f"{s.join(group.split(' '))}"
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+ o = f"msd_{type}_{name}.dat"
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  header = ''
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  msd_cols = []
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  for i in range(MSD.n_particles):
{mdkits-1.0.5 → mdkits-1.0.7}/LICENSE RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/README.md RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/__init__.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/convert.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/data.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/extract.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/cli/plot.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/rdf.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/vac.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/md_cli/wrap.py RENAMED
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{mdkits-1.0.5 → mdkits-1.0.7}/src/mdkits/mdkits.py RENAMED
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