orto 0.25.1__tar.gz → 0.26.1__tar.gz

{orto-0.25.1 → orto-0.26.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.25.1
+Version: 0.26.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://gitlab.com/kragskow-group/orto
 Author: Jon Kragskow

orto-0.26.1/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '0.26.1'

{orto-0.25.1 → orto-0.26.1}/orto/cli.py

@@ -13,6 +13,11 @@ import scipy.constants as constants
 import numpy as np
 import extto
 import docx
+import re
+import mmap
+import shutil
+
+
 from docx.enum.text import WD_ALIGN_PARAGRAPH
 from docx.enum.table import WD_ALIGN_VERTICAL
 from docx.shared import Pt
@@ -347,10 +352,57 @@ def gen_trunc_molden_func(uargs):
     None
     '''
 
-    # Read molden file in with regex
+    # Read molden file in as binary string
+    # and find number of MOs by counting number of
+    # occurrences of 'Occup='
+    _patt = re.compile(b'Sym=')
+    with open(uargs.input_file, mode="r") as file_obj:
+        with mmap.mmap(file_obj.fileno(), length=0, access=mmap.ACCESS_READ) as mmap_obj: # noqa
+            n_MO = len(_patt.findall(mmap_obj))
+
+    _patt = re.compile(b'Occup= 0.000000')
+    with open(uargs.input_file, mode="r") as file_obj:
+        with mmap.mmap(file_obj.fileno(), length=0, access=mmap.ACCESS_READ) as mmap_obj: # noqa
+            n_virt = len(_patt.findall(mmap_obj))
+
+    ut.cprint(
+        (
+            f'{n_virt}/{n_MO} MOs are virtual...'
+        ),
+        'cyan'
+    )
+
+    if uargs.output_file is None:
+        # If no output file specified, use input file name
+        # with .molden extension
+        uargs.output_file = '.tmp.molden'
+
+    # Trim file
+    _count = 0
+    final = False
+    with open(uargs.input_file, mode="r") as old:
+        with open(uargs.output_file, mode="w") as new:
+            # Read in molden file line by line
+            for line in old:
+                if 'Occup= 0.000000' in line:
+                    _count += 1
+                if _count == uargs.n_virt:
+                    final = True
+                if line.startswith(f'{n_MO:d}') and final:
+                    new.write(line)
+                    break
+                else:
+                    new.write(line)
+
+    ut.cprint(f'... trimming to {uargs.n_virt} virtual orbitals\n', 'cyan')
 
-    # Get number of basis functions
+    # If no output file given
+    if uargs.output_file == '.tmp.molden':
+        # Copy new file to original name
+        shutil.move(uargs.output_file, uargs.input_file)
+        uargs.output_file = uargs.input_file
 
+    ut.cprint(f'New molden file written to {uargs.output_file}', 'cyan')
 
     return
 
@@ -468,6 +520,9 @@ def gen_job_func(uargs):
         # Add call to orca_2mkl to create molden file from gbw
         if not uargs.no_molden:
             oj.post_orca += 'orca_2mkl {} -molden'.format(oj.input_file.stem)
+            oj.post_orca += '\norto gen trunc_molden {}.molden.input'.format(
+                oj.input_file.stem
+            )
 
         # Write job script
         # with submitter configuration options specified
@@ -798,7 +853,7 @@ def extract_orbs_func(uargs, save=True) -> None:
         _output = ''
         for row, val in mo.items():
             if val > uargs.threshold and row[1] in uargs.elements:
-                _output += f'  {row[1]+str(row[0]):5} {row[2]:5} : {val:>5.1f} %\n'
+                _output += f'  {row[1]+str(row[0]):5} {row[2]:5} : {val:>5.1f} %\n' # noqa
         if len(_output):
             print(_output)
 
@@ -1306,6 +1361,40 @@ def read_args(arg_list=None):
     # If argument list is empty then call help function
     gen_subprog.set_defaults(func=lambda _: gen_subprog.print_help())
 
+    gen_trunc_molden = gen_parser.add_parser(
+        'trunc_molden',
+        description='Generate truncated molden file',
+        usage=ut.cstring('orto gen trunc_molden <input_file> [options]', 'cyan'), # noqa
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    gen_trunc_molden._positionals.title = 'Mandatory Arguments'
+    gen_trunc_molden.set_defaults(func=gen_trunc_molden_func)
+    gen_trunc_molden.add_argument(
+        'input_file',
+        type=pathlib.Path,
+        help='Name of molden file to truncate'
+    )
+
+    gen_trunc_molden.add_argument(
+        '--output_file',
+        type=pathlib.Path,
+        help=(
+            'Name of truncated molden file',
+            'If not specified, molden file will be truncated in place'
+        ),
+        default=None
+    )
+
+    gen_trunc_molden.add_argument(
+        '--n_virt',
+        type=int,
+        default=100,
+        help=(
+            'Number of virtual orbitals to keep in truncated molden file\n'
+            'Default: %(default)s'
+        )
+    )
+
     gen_job = gen_parser.add_parser(
         'job',
         description=(

{orto-0.25.1 → orto-0.26.1}/orto/extractor.py

@@ -574,6 +574,7 @@ class FrequencyExtractor(extto.BetweenExtractor):
 
         # Calculate A_e in units of m mol^-1
         ae = np.ones_like(wavenumbers)
+        ae[:n_zero] = 0
         ae *= sc.Avogadro / (12 * sc.epsilon_0 * sc.speed_of_light**2)
         ae[n_zero:] *= t[n_zero:] ** 2
         # and convert to km mol^-1

{orto-0.25.1 → orto-0.26.1}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.25.1
+Version: 0.26.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://gitlab.com/kragskow-group/orto
 Author: Jon Kragskow

{orto-0.25.1 → orto-0.26.1}/setup.py

@@ -8,7 +8,7 @@ Please see the `orto` documentation for more details.
 
 # DO NOT EDIT THIS NUMBER!
 # IT IS AUTOMATICALLY CHANGED BY python-semantic-release
-__version__ = '0.25.1'
+__version__ = '0.26.1'
 
 setuptools.setup(
     name='orto',

orto-0.25.1/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '0.25.1'