mdkits 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

mdkits/build_cli/adsorbate.py

@@ -45,7 +45,7 @@ def main(atoms, adsorbate, cell, select, height, rotate, offset, cover):
 
     atoms.write(output_filename, format='cif')
 
-    print(os.path.abspath(output_filename))
+    out_err.path_output(output_filename)
 
 
 if __name__ == '__main__':

mdkits/build_cli/build_bulk.py

@@ -3,6 +3,7 @@
 import click, os
 from ase.build import bulk
 import numpy as np
+from mdkits.util import out_err
 
 
 @click.command(name='bulk')
@@ -29,7 +30,7 @@ def main(symbol, cs, a, b, c, alpha, covera, u, orth, cubic):
 
     o = f"{symbol}_{cs}.cif"
     atoms.write(o, format='cif')
-    print(os.path.abspath(o))
+    out_err.path_output(o)
 
 
 if __name__ == '__main__':

mdkits/build_cli/build_interface.py

@@ -23,6 +23,9 @@ def main(slab, sol, interval, cap, vacuum):
         slab_copy = slab.copy()
 
     sol_cell = sol.cell.cellpar()
+
+    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])]
+
     sol.set_pbc(True)
     sol.center()
     sol.positions[:, 2] += slab_cell[2] + interval
@@ -62,6 +65,8 @@ def main(slab, sol, interval, cap, vacuum):
         slab.set_cell(slab_cell)
         slab.center()
     
+    slab_cell[0] = interface_cell[0]
+    slab_cell[1] = interface_cell[1]
     if vacuum > 0:
         slab_cell[2] += vacuum
         slab.set_cell(slab_cell)

mdkits/build_cli/build_surface.py

@@ -50,7 +50,7 @@ def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum):
     
     out_err.check_cell(atoms)
     atoms.write(out_filename)
-    print(os.path.abspath(out_filename))
+    out_err.path_output(out_filename)
 
 
 if __name__ == '__main__':

mdkits/build_cli/supercell.py

@@ -34,7 +34,7 @@ def main(atoms, super, cell):
 
     o = f"{atoms.filename.split('.')[-2]}_{super[0]}{super[1]}{super[2]}.cif"
     super_atom.write(o)
-    print(os.path.abspath(o))
+    out_err.path_output(o)
 
 
 if __name__ == '__main__':

mdkits/cli/convert.py

@@ -57,7 +57,7 @@ def main(atoms, c, x, d, v, coord, cp2k, center, cell):
             f.write(f"ALPHA_BETA_GAMMA {cell[3]} {cell[4]} {cell[5]}\n")
 
 
-    print(os.path.abspath(o))
+    out_err.path_output(o)
 
 
 if __name__ == '__main__':

mdkits/cli/extract.py

@@ -4,7 +4,7 @@
 
 import os
 import click
-from mdkits.util import os_operation, arg_type
+from mdkits.util import os_operation, arg_type, out_err
 import MDAnalysis
 from MDAnalysis import Universe
 
@@ -84,7 +84,7 @@ def main(input_file_name, r, c, select):
     else:
         o = f"{os.path.basename(u.filename).split('.')[0]}_{'_'.join([str(i) for i in r])}_{'_'.join(select.split()) if select else 'all'}.xyz"
         write_to_xyz(u, frames, o, select, cut=cut)
-        click.echo(os.path.abspath(o))
+        out_err.path_output(o)
 
 
 if __name__ == '__main__':

mdkits/md_cli/msd.py

@@ -2,17 +2,25 @@ import click
 import MDAnalysis as mda
 import MDAnalysis.analysis.msd as msd
 import numpy as np
+from mdkits.util import arg_type
 
 
 @click.command(name="msd")
 @click.argument("filename", type=click.Path(exists=True))
 @click.argument('type', type=click.Choice(['xyz', 'xy', 'yz', 'xz', 'x', 'y', 'z']))
 @click.argument("group", type=str)
-def main(filename, type, group):
+@click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')
+def main(filename, type, group, r):
     """analysis msd along the given axis"""
     u = mda.Universe(filename)
     MSD = msd.EinsteinMSD(u, select=group, msd_type=type, fft=True)
-    MSD.run(verbose=True)
+    if r is not None:
+        if len(r) == 2:
+            MSD.run(start=r[0], stop=r[1], verbose=True)
+        elif len(r) == 3:
+            MSD.run(start=r[0], stop=r[1], step=r[2], verbose=True)
+    else:
+        MSD.run(verbose=True)
 
     data = np.arange(1, MSD.n_frames + 1).reshape(-1, 1)
     s = "_"

mdkits/md_cli/wrap.py

@@ -6,7 +6,8 @@ import MDAnalysis, click
 from mdkits.util import (
     arg_type,
     os_operation,
-    cp2k_input_parsing
+    cp2k_input_parsing,
+    out_err
     )
 
 
@@ -29,7 +30,7 @@ def main(filename, o, cell):
             W.write(ag)
 
     click.echo(f"\nwrap is done, output file {o} is:")
-    click.echo(os.path.abspath(o))
+    out_err.path_output(o)
 
 
 if __name__ == '__main__':

mdkits/util/out_err.py

@@ -14,7 +14,12 @@ def cell_output(atoms):
 
 
 def path_output(file: str):
-    print(os.path.abspath(file))
+    env_var_name = 'ssh_name'
+    file_path = os.path.abspath(file)
+    if os.environ.get(env_var_name):
+        ssh_name = os.environ.get(env_var_name)
+        file_path = f"{ssh_name}:{file_path}"
+    print(file_path)
 
 def check_cell(atoms, cell=None):
     if cell is not None:
@@ -26,4 +31,4 @@ def check_cell(atoms, cell=None):
         atoms.set_cell(cell)
         cell_output(atoms)
     else:
-        raise ValueError("can't parse cell please use --cell set cell")
+        raise ValueError("can't parse cell please use --cell set cell")

{mdkits-1.0.7.dist-info → mdkits-1.0.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 1.0.7
+Version: 1.0.9
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-1.0.7.dist-info → mdkits-1.0.9.dist-info}/RECORD

@@ -1,17 +1,17 @@
 mdkits/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mdkits/build_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mdkits/build_cli/adsorbate.py,sha256=9D_IYpnXd30pALC6JIvVPPxuxDfpsoArgMhE2hSeOSw,1947
-mdkits/build_cli/build_bulk.py,sha256=o3SFov5Ggk-qKcy6-NBoIYKvZV24OhcH3-du1d0U6H4,1593
+mdkits/build_cli/adsorbate.py,sha256=_Re942ZrHowcsOnBCjRAzkS-eYPWOZEZ5w5PmMztQ7Q,1944
+mdkits/build_cli/build_bulk.py,sha256=5sYnae68bFmo3IAcXFBTi7nJ1hTJKigxuWymRMkNKr8,1622
 mdkits/build_cli/build_cli.py,sha256=sqjnq5aHWLYLbNzN5SORkEYeYaewLagFuSvspJxyh7E,725
-mdkits/build_cli/build_interface.py,sha256=3EDxUb-vGHFuat1Ex_wojVsN8PtzHiGrnDQIEa9WZ60,2448
+mdkits/build_cli/build_interface.py,sha256=Lknbn2-xs7fTkr2ks-v1fGUFj-2S0DeFNvVkJknBAoc,2743
 mdkits/build_cli/build_solution.py,sha256=7bwaDH-vLBNRzGoYXT72bzLVXdQAZ4HXNuUDuR7AI78,5377
-mdkits/build_cli/build_surface.py,sha256=9GGpmQlCG6vxNevMyWcfI2EL_JiAAKIhxNokZyEzVLU,2739
+mdkits/build_cli/build_surface.py,sha256=KBQn8esurXcLFswRVddksot5Jii-jEm-egxq4p1w-DQ,2736
 mdkits/build_cli/cut_surface.py,sha256=_f0t2OyBKb8ZV04b3GezfSDUN4XFd5kQM-yWbSmOofs,2742
-mdkits/build_cli/supercell.py,sha256=3iTTt3DHaERWDFonhBRS0oqWhjFh6pbS5SpIR-O1gYg,1034
+mdkits/build_cli/supercell.py,sha256=ajB0ZbGtq0BFiOqD5ZqqLR7XE4jiINsfIHhshk_EDpo,1031
 mdkits/build_cli/water.xyz,sha256=ByLDz-rYhw_wLPBU78lIQHe4s4Xf5Ckjft-Dus3czIc,171
-mdkits/cli/convert.py,sha256=OmQ-7hmw0imgfgCJaWFEy3ePixsU7VKf0mGuJ6jRpn0,1795
+mdkits/cli/convert.py,sha256=f0GQQ-hPbJKhMwpITST7sj_LlrCkLdGB4UZY7lpbQsc,1792
 mdkits/cli/data.py,sha256=FGA4S9Cfo6WUJBSPWKOJrrZXHo_Qza-jNG1P_Dw7yi4,3262
-mdkits/cli/extract.py,sha256=dNf05CZuir98Z0EOjE33JrYK5_YBYLzuOauIt2Lwoh0,2944
+mdkits/cli/extract.py,sha256=33P9DXOUK38ORNZ3f-7Sx-1MCK9J0MIi1mqXHC9Pou0,2945
 mdkits/cli/plot.py,sha256=1yh5dq5jnQDuyWlxV_9g5ztsnuFHVu4ouYQ9VJYSrUU,8938
 mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
@@ -25,11 +25,11 @@ mdkits/md_cli/dipole.py,sha256=u_22-vMlzSEqGSpC6c5PG5t3uyjxaRKUvybgytovMk0,5027
 mdkits/md_cli/hb_distribution.py,sha256=lADOBiJYHCHPutXimXVDQpPdRKasBpldhiIl9SKf39o,7950
 mdkits/md_cli/md_cli.py,sha256=2vH04o_3d5kCJsn3qEq-iUPhebKJOrS-e7HJtyiZTiQ,571
 mdkits/md_cli/monitor.py,sha256=JNEgz5RGbFn4x_E85pAiPUY1NVIyZ3b2vjpBk_d1dR8,4536
-mdkits/md_cli/msd.py,sha256=yzBOeiVrYlTGwtttKNDr7kgooUEFoFCEhc7UZoWpXDM,1179
+mdkits/md_cli/msd.py,sha256=xg_c2sxNDOlxwK8jsNsQ4nbdqQAUvPGhOqFA6TXBTfs,1515
 mdkits/md_cli/rdf.py,sha256=p4HMMYZLfFRPnGx7YHQU6kZnMAfoL6vOyOVpZhfdBfM,1712
 mdkits/md_cli/setting.py,sha256=mxMTYpm6DUjMt9hOKsJbBSKwCqzMilOR0bo1azSdJP0,846
 mdkits/md_cli/vac.py,sha256=MJi_uftl0UUqhWvqDtcr14qtcRgYRd6X0VSg4J5MFN8,2133
-mdkits/md_cli/wrap.py,sha256=YdUpvhRyKn7bYnIAVgP39qItPdrEoTeJl55TmbS7Qqk,1044
+mdkits/md_cli/wrap.py,sha256=dwlLTfSnR5v99QP1klbbzWLXa71uQqprl7nSoVAm9dA,1049
 mdkits/mdkits.py,sha256=EiAt7dxGTaHuuj7bCNxgAqZbX0i3sldO0mBxOG-aMnY,595
 mdkits/util/.fig_operation.py.swp,sha256=iZYqdYMj4UKS1rmbXv8Ve2FcVBcNljX7Y43-neMdPSk,12288
 mdkits/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -40,10 +40,10 @@ mdkits/util/encapsulated_mda.py,sha256=m3i-XrcscMcM5V7JzLnor3JtAOfuDx3LLMl0tZt0n
 mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,1045
 mdkits/util/numpy_geo.py,sha256=B2QVADl1M8iixZrIOre2UUhHqvAeghvM8Q2woEQsH3Q,3880
 mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
-mdkits/util/out_err.py,sha256=7vGDI7wVoJWe1S0BDbcq-UC2KAhblCzg-NAYZKBZ4lo,900
+mdkits/util/out_err.py,sha256=GvHeXO5xHmTd5DK1QN6zvCSBBOUokM9DFdjsiDifxnc,1094
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-1.0.7.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-1.0.7.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-1.0.7.dist-info/METADATA,sha256=H_LUaRfw5rrrHB8q4vFD2dzrBoVn3wxWr9W581zZv_c,13539
-mdkits-1.0.7.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-1.0.7.dist-info/RECORD,,
+mdkits-1.0.9.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-1.0.9.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-1.0.9.dist-info/METADATA,sha256=9bwXyEI-9tAO3g0h5otgMItyqLbB4-6Ynu3P3fjiORA,13539
+mdkits-1.0.9.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-1.0.9.dist-info/RECORD,,