Moved ase_modules inside kinbot.

zadorlab · Jan 5, 2023 · bb5f672 · bb5f672
1 parent c9a915c
commit bb5f672
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Showing 17 changed files with 12 additions and 16 deletions.
diff --git a/kinbot/ase_modules/__init__.py b/kinbot/ase_modules/__init__.py
diff --git a/kinbot/ase_modules/calculators/__init__.py b/kinbot/ase_modules/calculators/__init__.py
diff --git a/ase_modules/calculators/gaussian.py → kinbot/ase_modules/calculators/gaussian.py b/ase_modules/calculators/gaussian.py → kinbot/ase_modules/calculators/gaussian.py
@@ -5,7 +5,7 @@
 from typing import Dict, Optional
 
 from ase.calculators.calculator import FileIOCalculator
-from ase_modules.io.formats import read, write
+from kinbot.ase_modules.io.formats import read, write
 
 
 class GaussianDynamics:

diff --git a/ase_modules/calculators/qchem.py → kinbot/ase_modules/calculators/qchem.py b/ase_modules/calculators/qchem.py → kinbot/ase_modules/calculators/qchem.py
diff --git a/ase_modules/constraints.py → kinbot/ase_modules/constraints.py b/ase_modules/constraints.py → kinbot/ase_modules/constraints.py
diff --git a/kinbot/ase_modules/io/__init__.py b/kinbot/ase_modules/io/__init__.py
diff --git a/ase_modules/io/formats.py → kinbot/ase_modules/io/formats.py b/ase_modules/io/formats.py → kinbot/ase_modules/io/formats.py
@@ -258,7 +258,7 @@ def define_io_format(name, desc, code, *, module=None, ext=None,
         module = name.replace('-', '_')
         format2modulename[name] = module
     if 'gaussian' in name:
-        module = 'ase_modules.io.' + module
+        module = 'kinbot.ase_modules.io.' + module
     else:
         module = 'ase.io.' + module
 

diff --git a/ase_modules/io/gaussian.py → kinbot/ase_modules/io/gaussian.py b/ase_modules/io/gaussian.py → kinbot/ase_modules/io/gaussian.py
@@ -14,7 +14,7 @@
 try:
     from ase.io.zmatrix import parse_zmatrix
 except ModuleNotFoundError:
-    from ase_modules.io.zmatrix import parse_zmatrix
+    from kinbot.ase_modules.io.zmatrix import parse_zmatrix
 
 _link0_keys = [
     'mem',

diff --git a/ase_modules/io/zmatrix.py → kinbot/ase_modules/io/zmatrix.py b/ase_modules/io/zmatrix.py → kinbot/ase_modules/io/zmatrix.py
diff --git a/kinbot/utils.py b/kinbot/utils.py
@@ -93,7 +93,7 @@ def clean_files():
     """
     import logging
     import numpy as np
-    from ase_modules.io.formats import read, write
+    from kinbot.ase_modules.io.formats import read
     # delete leftover AM1 calculations
     files = os.listdir()
     com = []

diff --git a/tpl/ase_gauss_hir.tpl.py b/tpl/ase_gauss_hir.tpl.py
@@ -2,7 +2,7 @@
 # from ase.calculators.gaussian import Gaussian
 from ase.db import connect
 
-from ase_modules.calculators.gaussian import Gaussian  # New
+from kinbot.ase_modules.calculators.gaussian import Gaussian  # New
 from kinbot import reader_gauss
 from kinbot.utils import iowait
 

diff --git a/tpl/ase_gauss_irc.tpl.py b/tpl/ase_gauss_irc.tpl.py
@@ -2,7 +2,7 @@
 # from ase.calculators.gaussian import Gaussian
 from ase.db import connect
 
-from ase_modules.calculators.gaussian import Gaussian  # New
+from kinbot.ase_modules.calculators.gaussian import Gaussian  # New
 from kinbot import reader_gauss
 from kinbot.utils import iowait
 

diff --git a/tpl/ase_gauss_opt_well.tpl.py b/tpl/ase_gauss_opt_well.tpl.py
@@ -3,7 +3,7 @@
 # from ase.calculators.gaussian import Gaussian
 from ase.db import connect
 
-from ase_modules.calculators.gaussian import Gaussian  # New
+from kinbot.ase_modules.calculators.gaussian import Gaussian  # New
 from kinbot import reader_gauss
 from kinbot.utils import iowait
 

diff --git a/tpl/ase_gauss_ring_conf.tpl.py b/tpl/ase_gauss_ring_conf.tpl.py
@@ -2,8 +2,8 @@
 from ase.optimize import LBFGS
 from ase.db import connect
 
-from ase_modules.calculators.gaussian import Gaussian
-from ase_modules.constraints import FixInternals  # New
+from kinbot.ase_modules.calculators.gaussian import Gaussian
+from kinbot.ase_modules.constraints import FixInternals  # New
 from kinbot import reader_gauss
 from kinbot.utils import iowait
 

diff --git a/tpl/ase_gauss_ts_end.tpl.py b/tpl/ase_gauss_ts_end.tpl.py
@@ -3,7 +3,7 @@
 #from ase.calculators.gaussian import Gaussian
 from ase.db import connect
 
-from ase_modules.calculators.gaussian import Gaussian  # New
+from kinbot.ase_modules.calculators.gaussian import Gaussian  # New
 from kinbot import reader_gauss
 from kinbot.utils import iowait
 

diff --git a/tpl/ase_gauss_ts_search.tpl.py b/tpl/ase_gauss_ts_search.tpl.py
@@ -2,7 +2,7 @@
 # from ase.calculators.gaussian import Gaussian
 from ase.db import connect
 
-from ase_modules.calculators.gaussian import Gaussian  # New
+from kinbot.ase_modules.calculators.gaussian import Gaussian  # New
 from kinbot import reader_gauss
 from kinbot.utils import iowait
 

diff --git a/tpl/ase_nwchem_ts_search_ase_constraints.tpl.py b/tpl/ase_nwchem_ts_search_ase_constraints.tpl.py
@@ -12,17 +12,13 @@
     c. Release: The coordinates to release (only for gaussian)
 """
 
-import os, sys, re
-
 from math import pi
-import numpy as np
 
-import ase
 from ase import Atoms
 from ase.calculators.nwchem import NWChem
 from ase.optimize import BFGS
 from ase.db import connect
-from ase_modules.constraints import FixInternals
+from kinbot.ase_modules.constraints import FixInternals
 
 label = '{label}'
 kwargs = {kwargs}