mdkits 1.0.8__py3-none-any.whl → 1.0.9__py3-none-any.whl

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Files changed (14) hide show
  1. mdkits/build_cli/adsorbate.py +1 -1
  2. mdkits/build_cli/build_bulk.py +2 -1
  3. mdkits/build_cli/build_interface.py +5 -0
  4. mdkits/build_cli/build_surface.py +1 -1
  5. mdkits/build_cli/supercell.py +1 -1
  6. mdkits/cli/convert.py +1 -1
  7. mdkits/cli/extract.py +2 -2
  8. mdkits/md_cli/wrap.py +3 -2
  9. mdkits/util/out_err.py +7 -2
  10. {mdkits-1.0.8.dist-info → mdkits-1.0.9.dist-info}/METADATA +1 -1
  11. {mdkits-1.0.8.dist-info → mdkits-1.0.9.dist-info}/RECORD +14 -14
  12. {mdkits-1.0.8.dist-info → mdkits-1.0.9.dist-info}/LICENSE +0 -0
  13. {mdkits-1.0.8.dist-info → mdkits-1.0.9.dist-info}/WHEEL +0 -0
  14. {mdkits-1.0.8.dist-info → mdkits-1.0.9.dist-info}/entry_points.txt +0 -0
mdkits/build_cli/adsorbate.py CHANGED
@@ -45,7 +45,7 @@ def main(atoms, adsorbate, cell, select, height, rotate, offset, cover):
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  atoms.write(output_filename, format='cif')
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- print(os.path.abspath(output_filename))
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+ out_err.path_output(output_filename)
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  if __name__ == '__main__':
mdkits/build_cli/build_bulk.py CHANGED
@@ -3,6 +3,7 @@
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  import click, os
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  from ase.build import bulk
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  import numpy as np
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+ from mdkits.util import out_err
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  @click.command(name='bulk')
@@ -29,7 +30,7 @@ def main(symbol, cs, a, b, c, alpha, covera, u, orth, cubic):
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  o = f"{symbol}_{cs}.cif"
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  atoms.write(o, format='cif')
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- print(os.path.abspath(o))
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+ out_err.path_output(o)
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  if __name__ == '__main__':
mdkits/build_cli/build_interface.py CHANGED
@@ -23,6 +23,9 @@ def main(slab, sol, interval, cap, vacuum):
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  slab_copy = slab.copy()
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  sol_cell = sol.cell.cellpar()
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+
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+ interface_cell = [max(slab_cell[0], sol_cell[0]), max(slab_cell[1], sol_cell[1]), max(slab_cell[2], sol_cell[2]), max(slab_cell[3], sol_cell[3]), max(slab_cell[4], sol_cell[4]), max(slab_cell[5], sol_cell[5])]
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+
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  sol.set_pbc(True)
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  sol.center()
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  sol.positions[:, 2] += slab_cell[2] + interval
@@ -62,6 +65,8 @@ def main(slab, sol, interval, cap, vacuum):
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  slab.set_cell(slab_cell)
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  slab.center()
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+ slab_cell[0] = interface_cell[0]
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+ slab_cell[1] = interface_cell[1]
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  if vacuum > 0:
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  slab_cell[2] += vacuum
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  slab.set_cell(slab_cell)
mdkits/build_cli/build_surface.py CHANGED
@@ -50,7 +50,7 @@ def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum):
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  out_err.check_cell(atoms)
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  atoms.write(out_filename)
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- print(os.path.abspath(out_filename))
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+ out_err.path_output(out_filename)
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  if __name__ == '__main__':
mdkits/build_cli/supercell.py CHANGED
@@ -34,7 +34,7 @@ def main(atoms, super, cell):
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  o = f"{atoms.filename.split('.')[-2]}_{super[0]}{super[1]}{super[2]}.cif"
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  super_atom.write(o)
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- print(os.path.abspath(o))
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+ out_err.path_output(o)
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  if __name__ == '__main__':
mdkits/cli/convert.py CHANGED
@@ -57,7 +57,7 @@ def main(atoms, c, x, d, v, coord, cp2k, center, cell):
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  f.write(f"ALPHA_BETA_GAMMA {cell[3]} {cell[4]} {cell[5]}\n")
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- print(os.path.abspath(o))
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+ out_err.path_output(o)
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  if __name__ == '__main__':
mdkits/cli/extract.py CHANGED
@@ -4,7 +4,7 @@
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  import os
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  import click
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- from mdkits.util import os_operation, arg_type
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+ from mdkits.util import os_operation, arg_type, out_err
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  import MDAnalysis
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  from MDAnalysis import Universe
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@@ -84,7 +84,7 @@ def main(input_file_name, r, c, select):
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  else:
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  o = f"{os.path.basename(u.filename).split('.')[0]}_{'_'.join([str(i) for i in r])}_{'_'.join(select.split()) if select else 'all'}.xyz"
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  write_to_xyz(u, frames, o, select, cut=cut)
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- click.echo(os.path.abspath(o))
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+ out_err.path_output(o)
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  if __name__ == '__main__':
mdkits/md_cli/wrap.py CHANGED
@@ -6,7 +6,8 @@ import MDAnalysis, click
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  from mdkits.util import (
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  arg_type,
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  os_operation,
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- cp2k_input_parsing
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+ cp2k_input_parsing,
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+ out_err
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  )
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@@ -29,7 +30,7 @@ def main(filename, o, cell):
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  W.write(ag)
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  click.echo(f"\nwrap is done, output file {o} is:")
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- click.echo(os.path.abspath(o))
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+ out_err.path_output(o)
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  if __name__ == '__main__':
mdkits/util/out_err.py CHANGED
@@ -14,7 +14,12 @@ def cell_output(atoms):
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  def path_output(file: str):
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- print(os.path.abspath(file))
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+ env_var_name = 'ssh_name'
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+ file_path = os.path.abspath(file)
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+ if os.environ.get(env_var_name):
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+ ssh_name = os.environ.get(env_var_name)
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+ file_path = f"{ssh_name}:{file_path}"
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+ print(file_path)
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  def check_cell(atoms, cell=None):
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  if cell is not None:
@@ -26,4 +31,4 @@ def check_cell(atoms, cell=None):
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  atoms.set_cell(cell)
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  cell_output(atoms)
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  else:
29
- raise ValueError("can't parse cell please use --cell set cell")
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+ raise ValueError("can't parse cell please use --cell set cell")
{mdkits-1.0.8.dist-info → mdkits-1.0.9.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: mdkits
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- Version: 1.0.8
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+ Version: 1.0.9
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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-1.0.8.dist-info → mdkits-1.0.9.dist-info}/RECORD RENAMED
@@ -1,17 +1,17 @@
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  mdkits/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
2
  mdkits/build_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
3
- mdkits/build_cli/adsorbate.py,sha256=9D_IYpnXd30pALC6JIvVPPxuxDfpsoArgMhE2hSeOSw,1947
4
- mdkits/build_cli/build_bulk.py,sha256=o3SFov5Ggk-qKcy6-NBoIYKvZV24OhcH3-du1d0U6H4,1593
3
+ mdkits/build_cli/adsorbate.py,sha256=_Re942ZrHowcsOnBCjRAzkS-eYPWOZEZ5w5PmMztQ7Q,1944
4
+ mdkits/build_cli/build_bulk.py,sha256=5sYnae68bFmo3IAcXFBTi7nJ1hTJKigxuWymRMkNKr8,1622
5
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  mdkits/build_cli/build_cli.py,sha256=sqjnq5aHWLYLbNzN5SORkEYeYaewLagFuSvspJxyh7E,725
6
- mdkits/build_cli/build_interface.py,sha256=3EDxUb-vGHFuat1Ex_wojVsN8PtzHiGrnDQIEa9WZ60,2448
6
+ mdkits/build_cli/build_interface.py,sha256=Lknbn2-xs7fTkr2ks-v1fGUFj-2S0DeFNvVkJknBAoc,2743
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  mdkits/build_cli/build_solution.py,sha256=7bwaDH-vLBNRzGoYXT72bzLVXdQAZ4HXNuUDuR7AI78,5377
8
- mdkits/build_cli/build_surface.py,sha256=9GGpmQlCG6vxNevMyWcfI2EL_JiAAKIhxNokZyEzVLU,2739
8
+ mdkits/build_cli/build_surface.py,sha256=KBQn8esurXcLFswRVddksot5Jii-jEm-egxq4p1w-DQ,2736
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  mdkits/build_cli/cut_surface.py,sha256=_f0t2OyBKb8ZV04b3GezfSDUN4XFd5kQM-yWbSmOofs,2742
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- mdkits/build_cli/supercell.py,sha256=3iTTt3DHaERWDFonhBRS0oqWhjFh6pbS5SpIR-O1gYg,1034
10
+ mdkits/build_cli/supercell.py,sha256=ajB0ZbGtq0BFiOqD5ZqqLR7XE4jiINsfIHhshk_EDpo,1031
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  mdkits/build_cli/water.xyz,sha256=ByLDz-rYhw_wLPBU78lIQHe4s4Xf5Ckjft-Dus3czIc,171
12
- mdkits/cli/convert.py,sha256=OmQ-7hmw0imgfgCJaWFEy3ePixsU7VKf0mGuJ6jRpn0,1795
12
+ mdkits/cli/convert.py,sha256=f0GQQ-hPbJKhMwpITST7sj_LlrCkLdGB4UZY7lpbQsc,1792
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  mdkits/cli/data.py,sha256=FGA4S9Cfo6WUJBSPWKOJrrZXHo_Qza-jNG1P_Dw7yi4,3262
14
- mdkits/cli/extract.py,sha256=dNf05CZuir98Z0EOjE33JrYK5_YBYLzuOauIt2Lwoh0,2944
14
+ mdkits/cli/extract.py,sha256=33P9DXOUK38ORNZ3f-7Sx-1MCK9J0MIi1mqXHC9Pou0,2945
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  mdkits/cli/plot.py,sha256=1yh5dq5jnQDuyWlxV_9g5ztsnuFHVu4ouYQ9VJYSrUU,8938
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  mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
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  mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
@@ -29,7 +29,7 @@ mdkits/md_cli/msd.py,sha256=xg_c2sxNDOlxwK8jsNsQ4nbdqQAUvPGhOqFA6TXBTfs,1515
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  mdkits/md_cli/rdf.py,sha256=p4HMMYZLfFRPnGx7YHQU6kZnMAfoL6vOyOVpZhfdBfM,1712
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  mdkits/md_cli/setting.py,sha256=mxMTYpm6DUjMt9hOKsJbBSKwCqzMilOR0bo1azSdJP0,846
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  mdkits/md_cli/vac.py,sha256=MJi_uftl0UUqhWvqDtcr14qtcRgYRd6X0VSg4J5MFN8,2133
32
- mdkits/md_cli/wrap.py,sha256=YdUpvhRyKn7bYnIAVgP39qItPdrEoTeJl55TmbS7Qqk,1044
32
+ mdkits/md_cli/wrap.py,sha256=dwlLTfSnR5v99QP1klbbzWLXa71uQqprl7nSoVAm9dA,1049
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  mdkits/mdkits.py,sha256=EiAt7dxGTaHuuj7bCNxgAqZbX0i3sldO0mBxOG-aMnY,595
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  mdkits/util/.fig_operation.py.swp,sha256=iZYqdYMj4UKS1rmbXv8Ve2FcVBcNljX7Y43-neMdPSk,12288
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  mdkits/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -40,10 +40,10 @@ mdkits/util/encapsulated_mda.py,sha256=m3i-XrcscMcM5V7JzLnor3JtAOfuDx3LLMl0tZt0n
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  mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,1045
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  mdkits/util/numpy_geo.py,sha256=B2QVADl1M8iixZrIOre2UUhHqvAeghvM8Q2woEQsH3Q,3880
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  mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
43
- mdkits/util/out_err.py,sha256=7vGDI7wVoJWe1S0BDbcq-UC2KAhblCzg-NAYZKBZ4lo,900
43
+ mdkits/util/out_err.py,sha256=GvHeXO5xHmTd5DK1QN6zvCSBBOUokM9DFdjsiDifxnc,1094
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44
  mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
45
- mdkits-1.0.8.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
46
- mdkits-1.0.8.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
47
- mdkits-1.0.8.dist-info/METADATA,sha256=I8CmwQEDphRQRmtmhp0b6GJ76W54pIPLufV8SdWNXes,13539
48
- mdkits-1.0.8.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
49
- mdkits-1.0.8.dist-info/RECORD,,
45
+ mdkits-1.0.9.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
46
+ mdkits-1.0.9.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
47
+ mdkits-1.0.9.dist-info/METADATA,sha256=9bwXyEI-9tAO3g0h5otgMItyqLbB4-6Ynu3P3fjiORA,13539
48
+ mdkits-1.0.9.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
49
+ mdkits-1.0.9.dist-info/RECORD,,
{mdkits-1.0.8.dist-info → mdkits-1.0.9.dist-info}/WHEEL RENAMED
File without changes