mdkits 1.0.8__tar.gz → 1.0.9__tar.gz

{mdkits-1.0.8 → mdkits-1.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 1.0.8
+Version: 1.0.9
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-1.0.8 → mdkits-1.0.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "1.0.8"
+version = "1.0.9"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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-1.0.8 → mdkits-1.0.9}/src/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")