Im currently tryng to install tamkin using "pip install tamkin" and the folloring error appears,

Using cached tamkin-1.2.6.tar.gz (5.1 MB)
ERROR: The tar file (C:\Users\quimi\AppData\Local\Temp\pip-unpack-v752alsg\tamkin-1.2.6.tar.gz) has a file (C:\Users\quimi\AppData\Local\Temp\pip-install-7wn8272v\tamkin\doc/reference/aux.rst) trying to install outside target directory (C:\Users\quimi\AppData\Local\Temp\pip-install-7wn8272v\tamkin)

and advice in this topic would be really helpful, thanks in advance anda have a nice day.

New Text Document.txt

Dear developers,
Hi!

Do you have a plan to write a parser for Molpro outputs? We use Molpro to perform CCSD(T)-F12 calculation, which is accurate to give frequencies. It can be post-processed by TAMkin, especially using the NMA functions.

If you do not have spare time, I can write it and contribute.

Yours,
Yu

I ran the command 'pip install tamkin --user' and got the following lines.

Collecting tamkin
Requirement already satisfied: molmod>=1.3.2 in ./.local/lib/python3.5/site-packages (from tamkin) (1.4.4)
Requirement already satisfied: matplotlib>1.1 in /usr/lib/python3/dist-packages (from tamkin) (1.5.1)
Requirement already satisfied: numpy>=1.0 in ./.local/lib/python3.5/site-packages (from tamkin) (1.16.4)
Requirement already satisfied: nose>=0.11 in ./.local/lib/python3.5/site-packages (from tamkin) (1.3.7)
Collecting scipy>=0.17.1 (from tamkin)
Using cached https://files.pythonhosted.org/packages/14/49/8f13fa215e10a7ab0731cc95b0e9bb66cf83c6a98260b154cfbd0b55fb19/scipy-1.3.0-cp35-cp35m-manylinux1_x86_64.whl
Requirement already satisfied: future in ./.local/lib/python3.5/site-packages (from molmod>=1.3.2->tamkin) (0.17.1)
Requirement already satisfied: cython>=0.24.1 in ./.local/lib/python3.5/site-packages (from molmod>=1.3.2->tamkin) (0.29.12)
Installing collected packages: scipy, tamkin
Successfully installed scipy-1.3.0 tamkin-1.2.4

This looks like TAMkin has been successfully installed with other associated dependencies.

But when I run the command 'nosetests -v tamkin', it gives me an error saying

'The program 'nosetests' is currently not installed. You can install it by typing:
sudo apt install python-nose'

Kindly advice how to go about it.

Thanks

Dear Toon,

when installing conda install -c conda-forge molmod
or alternativelyy conda install -c molmod tamkin nose
it keeps giving me errors like:

(KoppScience) wk858834@login18-1:~[517]$ nosetests molmod    
E
======================================================================
ERROR: Failure: ValueError (numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wk858834/anaconda2/envs/KoppScience/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/home/wk858834/anaconda2/envs/KoppScience/lib/python3.7/site-packages/nose/loader.py", line 406, in loadTestsFromName
    module = resolve_name(addr.module)
  File "/home/wk858834/anaconda2/envs/KoppScience/lib/python3.7/site-packages/nose/util.py", line 312, in resolve_name
    module = __import__('.'.join(parts_copy))
  File "/home/wk858834/anaconda2/envs/KoppScience/lib/python3.7/site-packages/molmod/__init__.py", line 67, in <module>
    from molmod.similarity import *
  File "/home/wk858834/anaconda2/envs/KoppScience/lib/python3.7/site-packages/molmod/similarity.py", line 45, in <module>
    from molmod.ext import similarity_table_labels, similarity_table_distances, \
  File "__init__.pxd", line 918, in init molmod.ext
ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

----------------------------------------------------------------------
Ran 1 test in 0.002s

FAILED (errors=1)

Do you have an idea what is going wrong here?

Best Regards
Wassja

In its current version, the output printed by dump_modes_gaussian is not readable by Molden due to some minor bugs. More specifically:

• Line 241 should be print(' Frequencies --', end="", file=f) instead of print(' Frequencies --', file=f). Now, the word 'Frequencies' and the actual frequencies are written on separate lines, while they should be on the same line.
• Line 253 should be print('%9.2f %6.2f %6.2f' % ( instead of print('%8.2f %6.2f %6.2f' % (. i.e. an extra space is needed in front of the x coordinate.

On a clean install of tamkin under python3.8 on Ubuntu 20.04 LTS, the nosetest for timer.py fails:
EDIT: this issue was verified on Fedora 32 with python3.8

======================================================================
ERROR: test_timer (tamkin.test.test_timer.TimerTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/fuller/.local/lib/python3.8/site-packages/tamkin/test/test_timer.py", line 53, in test_timer
    timer.sample("start")
  File "/home/fuller/.local/lib/python3.8/site-packages/tamkin/timer.py", line 67, in sample
    self.cpu_times.append(time.clock())
AttributeError: module 'time' has no attribute 'clock'

----------------------------------------------------------------------
Ran 126 tests in 22.446s

FAILED (errors=1)

According to release information for python 3.8 (https://docs.python.org/3/whatsnew/3.8.html):

The function time.clock() has been removed, after having been deprecated since Python 3.3: use time.perf_counter() or time.process_time() instead, depending on your requirements, to have well-defined behavior. (Contributed by Matthias Bussonnier in bpo-36895.)

Similar to molmod/molmod#32. See https://github.com/conda-forge/tamkin-feedstock and https://anaconda.org/conda-forge/tamkin

Maybe there's a quick fix for this, but I noticed building and installing with pip that it allows building with Python >=3, but it uses Python 2 style print. I believe Python 3 has standardized print() to be like any function. So it just needs a quick run through with sed or awk to update it.

Correct me if I'm wrong.

After the successful installation, when I run "nosetests -v tamkin", I get the following message:

Ran 0 tests in 0.000s

OK

What is going on?

Hi,

I was wondering if TAMKIN can process NAMD files. I am interested to use TAMKIN for Normal Mode Analysis.

I will appreciate your response.

Mamta

As in the associated issue with Ubuntu (#26), the installation instructions for Fedora should be updated (tested on updated Fedora 32, 12 June 2020):

Recommend the installation instructions be updated as follows (https://molmod.github.io/tamkin/tutorial/install.html):

External dependencies:
sudo dnf install python3 python3-numpy python3-scipy python3-matplotlib python3-nose python3-Cython
As currently written, Cython are not installed automatically, leading to errors when attempting to install tamkin with pip.
Also, as currently written, scipy returns an error ("not found") and numpy prompts for install of python2-numpy
Also here it is my recommendation that the installation instructions be written for python3 to avoid python2, which has reached end-of-life.

Installation:
It is not be necessary to install numpy and nosetests with pip when installed systemwide under external dependencies.

Examples "004_alkanes" are failing after successful run of cp2k with following error:
"Could not read energy and/or gradient (forces) from single point file."
I used cp2k 6.1.0.

Hello,

I want to install the Tamkin software in my remote server in CDAC, Pune. Could you please help in installing this software.
I am doing frequency analysis of CO2 adsorbed systems over the slab surface using VASP. Now, I want to analyze thermodynamical properties of this system like Enthalpy, free energy, Gibbs free energy.
I find this Tamkin software very useful in calculating Thermodynamical properties. However, I am not able to Install it. I need guidance in installing and usage of this software.

Regards,
Seema Gautam

I think, 5T examples do not work.
Can you plese check.
Couldn't even load them onto Gaussview.

Hello Tamkin Community,
I wanted to ask if it is currently possible to read in/out ADF output files. In the PubMed publication it is stated that ADF output files are indeed supported although I cannot find any mention of ADF in the Documentation or anywhere else.

Any help would be much appreciated.

For a clean install on a fully updated Ubuntu 20.04 LTS (12 June 2020), recommend the installation instructions be updated as follows (https://molmod.github.io/tamkin/tutorial/install.html):

External dependencies:
sudo apt install python3 python3-numpy python3-scipy python3-matplotlib python3-nose python3-pip cython3
As currently written, pip and cython are not installed automatically, leading to errors when attempting to install tamkin with pip.
Also, as currently written with pythonand not python3, clean installs default to python2 and prompt to install python-is-python2 which sets system python to 2.x: It is my suggestion that the installation instructions be written for python3 to avoid setting the default to python 2, which has reached end-of-life.
EDIT: I am also recommending replacing apt-get by apt as this is a newer and preferred implementation for command-line package management in Ubuntu and Debian.

Installation:
It is not be necessary to install numpy and nosetests with pip when installed systemwide under external dependencies.

We are installing Tamkin 1.2.6 using Python 3.11.3, molmod 1.4.8, nose3 1.3.8 using GCC 12.3.0

When running the tests export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; export OMP_NUM_THREADS=1; nosetests -v tamkin we see the test_vsa_no_mass failing on 2 different architectures (power9le & x86 haswell) with similar differences:

FAIL: test_vsa_no_mass (tamkin.test.test_nma.NMATestCase.test_vsa_no_mass)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/dev/shm/s3248973-EasyBuild/TAMkin/1.2.6/foss-2023a/tamkin-1.2.6/tamkin/test/test_nma.py", line 532, in test_vsa_no_mass
    self.check_freqs(expected_freqs, nma, 0, check_zeros=True)
  File "/dev/shm/s3248973-EasyBuild/TAMkin/1.2.6/foss-2023a/tamkin-1.2.6/tamkin/test/test_nma.py", line 77, in check_freqs
    self.assertAlmostEqual(
AssertionError: 0.13774798 != 0.6608735502232888 within 0 places (0.5231255702232888 difference) : Frequency 2 does not match, expected - computed = 0.1 - 0.7 = -0.523126

======================================================================
FAIL: test_vsa_no_mass (tamkin.test.test_nma.NMATestCase.test_vsa_no_mass)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/boegelbot/TAMkin/1.2.6/foss-2023a/tamkin-1.2.6/tamkin/test/test_nma.py", line 532, in test_vsa_no_mass
    self.check_freqs(expected_freqs, nma, 0, check_zeros=True)
  File "/tmp/boegelbot/TAMkin/1.2.6/foss-2023a/tamkin-1.2.6/tamkin/test/test_nma.py", line 77, in check_freqs
    self.assertAlmostEqual(
AssertionError: 0.13774798 != 0.6460767049351539 within 0 places (0.5083287249351539 difference) : Frequency 2 does not match, expected - computed = 0.1 - 0.6 = -0.508329

Is this something to worry about or is this somehow "expected"?