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author
Guilian Luchini
authored
v3.2 (#60)
* Fixes a bug for parsing ORCA spc with MiniPrint * Updates for new release * Replace "bobbypaton" with "patonlab" for urls * Update tests
1 parent 8d29b55 commit c736a98

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Lines changed: 126 additions & 40 deletions

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‎.travis-install.sh‎

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -4,10 +4,6 @@ if [[$TRAVIS_OS_NAME == 'osx']]; then
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brew update
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brew install pyenv-virtualenv
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case "${TOXENV}" in
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py35)
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pyenv install 3.5.2
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export PYENV_VERSION=3.5.2
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;;
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py36)
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pyenv install 3.6.7
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export PYENV_VERSION=3.6.7
@@ -20,6 +16,14 @@ if [[$TRAVIS_OS_NAME == 'osx']]; then
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pyenv install 3.8.1
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export PYENV_VERSION=3.8.1
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;;
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py39)
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pyenv install 3.9
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export PYENV_VERSION=3.9
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;;
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py310)
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pyenv install 3.10
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export PYENV_VERSION=3.10
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;;
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esac
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export PATH="/Users/travis/.pyenv/shims:${PATH}"
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pyenv-virtualenv venv

‎.travis.yml‎

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@@ -4,34 +4,46 @@ dist: trusty
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matrix:
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include:
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- os: linux
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python: 3.5
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env: TOXENV=py35
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python: 3.6
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env: TOXENV=py36
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dist: trusty
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install:
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- "./.travis-install.sh"
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- pip install pytest
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- pip install --upgrade numpy
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- python -m pip install .
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script:
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- pytest -v
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- os: linux
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python: 3.6
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env: TOXENV=py36
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python: 3.8
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env: TOXENV=py38
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dist: xenial
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install:
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- "./.travis-install.sh"
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- pip install pytest
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- pip install --upgrade numpy
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- python -m pip install .
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script:
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- pytest -v
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- os: linux
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python: 3.8
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env: TOXENV=py38
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python: 3.9
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env: TOXENV=py39
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dist: xenial
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install:
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- "./.travis-install.sh"
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- pip install pytest
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- python -m pip install .
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script:
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- pytest -v
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- os: linux
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python: 3.10
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env: TOXENV=py310
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dist: focal
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install:
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- "./.travis-install.sh"
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- pip install pytest
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- python -m pip install .
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script:
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- pytest -v
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- os: osx
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language: generic
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env: TOXENV=py36
@@ -61,6 +73,26 @@ matrix:
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- python3 -m pip install .
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script:
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- pytest -v
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- os: osx
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language: generic
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env: TOXENV=py39
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dist: xenial
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install:
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- "./.travis-install.sh"
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- pip3 install pytest
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- python3 -m pip install .
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script:
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- pytest -v
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- os: osx
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language: generic
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env: TOXENV=py310
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dist: xenial
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install:
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- "./.travis-install.sh"
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- pip3 install pytest
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- python3 -m pip install .
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script:
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- pytest -v
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- os: windows
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language: shell
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before_install:
@@ -112,6 +144,40 @@ matrix:
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- python -m pip install .
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script:
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- pytest -v
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- os: windows
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language: shell
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before_install:
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- choco install python --version=3.9
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- python --version
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- python -m pip install --upgrade pip
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- pip install --upgrade pytest
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- pip install codecov
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- pip install numpy
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- pip install cython
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env: PATH=/c/Python39:/c/Python39/Scripts:$PATH
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install:
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- "./.travis-install.sh"
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- pip install pytest
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- python -m pip install .
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script:
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- pytest -v
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- os: windows
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language: shell
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before_install:
167+
- choco install python --version=3.10
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- python --version
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- python -m pip install --upgrade pip
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- pip install --upgrade pytest
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- pip install codecov
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- pip install numpy
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- pip install cython
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env: PATH=/c/Python310:/c/Python310/Scripts:$PATH
175+
install:
176+
- "./.travis-install.sh"
177+
- pip install pytest
178+
- python -m pip install .
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script:
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- pytest -v
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deploy:
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provider: pypi
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username: "__token__"

‎goodvibes/GoodVibes.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@
4949
########### Authors: Rob Paton, Ignacio Funes-Ardoiz ############
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########### Guilian Luchini, Juan V. Alegre- ############
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########### Requena, Yanfei Guan, Sibo Lin ############
52-
########### Last modified: May 27, 2020 ############
52+
########### Last modified: August 8, 2022 ############
5353
####################################################################"""
5454

5555
import math, os.path, sys, time
@@ -79,7 +79,7 @@
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pass
8080

8181
# VERSION NUMBER
82-
__version__ = "3.1.1"
82+
__version__ = "3.2"
8383

8484
SUPPORTED_EXTENSIONS = set(('.out', '.log'))
8585

‎goodvibes/io.py‎

Lines changed: 36 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -228,7 +228,7 @@ def parse_data(file):
228228
if os.path.exists(possible_filename):
229229
with open(possible_filename) as f:
230230
data = f.readlines()
231-
ccdata = ccread(possible_filename)
231+
232232
if data is None:
233233
raise ValueError("File {} does not exist".format(file))
234234

@@ -243,14 +243,28 @@ def parse_data(file):
243243
program = "NWChem"
244244
break
245245
repeated_link1 = 0
246-
spe = ccdata.scfenergies[-1]
247-
if hasattr(ccdata, "mpenergies"):
248-
spe = ccdata.mpenergies[-1]
249-
if hasattr(ccdata, "ccenergies"):
250-
spe = ccdata.ccenergies[-1]
251-
spe = convertor(spe, "eV", "hartree")
252-
charge = ccdata.charge
253-
multiplicity = ccdata.mult
246+
247+
if program != "Orca":
248+
try:
249+
possible_filenames = (stub + ".log", stub + ".out")
250+
for possible_filename in possible_filenames:
251+
if os.path.exists(possible_filename):
252+
ccdata = ccread(possible_filename)
253+
except IndexError:
254+
ccdata = None
255+
if ccdata:
256+
try:
257+
spe = ccdata.scfenergies[-1]
258+
if hasattr(ccdata, "mpenergies"):
259+
spe = ccdata.mpenergies[-1]
260+
if hasattr(ccdata, "ccenergies"):
261+
spe = ccdata.ccenergies[-1]
262+
spe = convertor(spe, "eV", "hartree")
263+
charge = ccdata.charge
264+
multiplicity = ccdata.mult
265+
except AttributeError:
266+
pass
267+
254268
for line in data:
255269
if program == "Gaussian":
256270
if line.strip().startswith('E2('):
@@ -282,9 +296,22 @@ def parse_data(file):
282296
elif program == "Orca":
283297
if 'Program Version' in line.strip():
284298
version_program = "ORCA version " + line.split()[2]
299+
if line.strip().startswith('FINAL SINGLE POINT ENERGY'):
300+
spe = float(line.strip().split()[4])
301+
if "Total Charge" in line.strip() and "...." in line.strip():
302+
charge = int(line.strip("=").split()[-1])
303+
if "Multiplicity" in line.strip() and "...." in line.strip():
304+
multiplicity = int(line.strip("=").split()[-1])
285305
elif program == "NWChem":
286306
if 'nwchem branch' in line.strip():
287307
version_program = "NWChem version " + line.split()[3]
308+
if ccdata == None:
309+
if line.strip().startswith('Total DFT energy'):
310+
spe = float(line.strip().split()[4])
311+
if "charge" in line.strip():
312+
charge = int(line.strip().split()[-1])
313+
if "mult " in line.strip():
314+
multiplicity = int(line.strip().split()[-1])
288315

289316
# Solvation model and empirical dispersion detection
290317
if 'Gaussian' in version_program.strip():
@@ -434,17 +461,6 @@ def parse_data(file):
434461
empirical_dispersion3 = ' with zero damping'
435462
empirical_dispersion = empirical_dispersion1 + empirical_dispersion2 + empirical_dispersion3
436463
if 'NWChem' in version_program.strip():
437-
# keyword_line_1 = "gas phase"
438-
# keyword_line_2 = ''
439-
# keyword_line_3 = ''
440-
# for i, line in enumerate(data):
441-
# if 'CPCM SOLVATION MODEL' in line.strip():
442-
# keyword_line_1 = "CPCM,"
443-
# if 'SMD CDS free energy correction energy' in line.strip():
444-
# keyword_line_2 = "SMD,"
445-
# if "Solvent: " in line.strip():
446-
# keyword_line_3 = line.strip().split()[-1]
447-
# solvation_model = keyword_line_1 + keyword_line_2 + keyword_line_3
448464
empirical_dispersion1 = 'No empirical dispersion detected'
449465
empirical_dispersion2 = ''
450466
empirical_dispersion3 = ''

‎goodvibes/pes.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -663,8 +663,8 @@ def graph_reaction_profile(graph_data, log, options, plt):
663663
[Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4]),
664664
fc="none", transform=ax.transData, color=color)
665665
ax.add_patch(path_patch)
666-
plt.hlines(data[path][j], j - 0.15, j + 0.15)
667-
plt.hlines(data[path][-1], len(data[path]) - 1.15, len(data[path]) - 0.85)
666+
plt.hlines(data[path][j], j - 0.15, j + 0.15,colors=['k'])
667+
plt.hlines(data[path][-1], len(data[path]) - 1.15, len(data[path]) - 0.85,colors=['k'])
668668

669669
if show_conf:
670670
markers = ['o', 's', 'x', 'P', 'D']

‎meta.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
{% set name = "goodvibes" %}
2-
{% set version = "3.1.1" %}
2+
{% set version = "3.2" %}
33

44
package:
55
name: "{{ name|lower }}"
@@ -27,7 +27,7 @@ test:
2727
- goodvibes
2828

2929
about:
30-
home: https://github.com/bobbypaton/goodvibes
30+
home: https://github.com/patonlab/goodvibes
3131
license: MIT
3232
license_family: MIT
3333
license_file: LICENSE.txt

‎setup.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -10,14 +10,14 @@
1010
setup(
1111
name='goodvibes',
1212
packages=['goodvibes'],
13-
version='3.1.1',
13+
version='3.2',
1414
description='A python program to compute corrections to thermochemical data from frequency calculations',
1515
long_description=long_description,
1616
long_description_content_type='text/markdown',
1717
author='Paton Research Group',
1818
author_email='robert.paton@colostate.edu',
19-
url='https://github.com/bobbypaton/goodvibes',
20-
download_url='https://github.com/bobbypaton/GoodVibes/archive/v3.1.1.zip',
19+
url='https://github.com/patonlab/goodvibes',
20+
download_url='https://github.com/patonlab/GoodVibes/archive/v3.2.zip',
2121
keywords=['compchem', 'thermochemistry', 'gaussian', 'vibrational-entropies', 'temperature'],
2222
classifiers=[],
2323
install_requires=['numpy','cclib'],

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