Light

molmod / yaff Goto Github PK

View Code? Open in Web Editor NEW

31.0 31.0 18.0 18.91 MB

Yaff is yet another force-field code

Home Page: http://molmod.github.io/yaff

License: GNU General Public License v3.0

Python 78.07% C 13.52% Batchfile 0.11% Shell 0.10% Cython 8.21%

yaff's Introduction

MolMod is a collection of molecular modelling tools for python. It is used by other software developed at the CMM, including Yaff, TAMkin and Zeobuilder.

More information about MolMod can be found on the CMM Code website: http://molmod.ugent.be/software

MolMod is distributed as open source software under the conditions of the GPL license version 3. Read the file COPYING for more details, or visit http://www.gnu.org/licenses/

Installation

MolMod can be installed with pip (system wide or in a virtual environment):

pip install Cython numpy
pip install molmod

Alternatively, you can install MolMod in your home directory:

pip install Cython numpy --user
pip install molmod --user

Lastly, you can also install MolMod with conda. (See https://www.continuum.io/downloads)

# Using the builds from Travis-CI ...
conda install -c molmod molmod
# ... or using the packages on conda-force
conda install -c conda-forge molmod

Testing

The tests can be executed as follows:

pytest molmod

yaff's People

Contributors

Stargazers

Watchers

Forkers

tovrstra stevenvdb svenrogge boegel lvduyfhu maaren yfyh2013 michaelsluydts sanderborgmans eneslievens aranlamaire zarasthustra jelle-w caiyingchun mcoolsce daemondevils jackevansadl elsenety

yaff's Issues

yaff 1.6.0 tests fail

I'm trying to build yaff 1.6.0 using Python 3.8.6, GCC 10.2.0, h5py 3.1.0.
I believe the error has to do something with my system but wanted to confirm with you and hear your opinion on what might have gone wrong.

I have many tests failing with:

======================================================================
ERROR: yaff.analysis.test.test_basic.test_plot_energies_nve
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/apps/USE/easybuild/staging/2021.1/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/test/test_basic.py", line 35, in test_plot_energies_nve
    with run_nve_water32(__name__, 'test_plot_energies_nve') as (dn_tmp, nve, f):
  File "/home/apps/USE/easybuild/staging/2021.1/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/contextlib.py", line 113, in __enter__
    return next(self.gen)
  File "/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/test/common.py", line 43, in run_nve_water32
    with h5.File('%s/output.h5' % dn_tmp) as f:
  File "/home/apps/USE/easybuild/staging/2021.1/software/h5py/3.1.0-foss-2020b/lib/python3.8/site-packages/h5py/_hl/files.py", line 424, in __init__
    fid = make_fid(name, mode, userblock_size,
  File "/home/apps/USE/easybuild/staging/2021.1/software/h5py/3.1.0-foss-2020b/lib/python3.8/site-packages/h5py/_hl/files.py", line 190, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 96, in h5py.h5f.open
OSError: Unable to open file (unable to open file: name = '/dev/shm/build/eb-8sh04g0l/test_plot_energies_nveujdetjpqyaff.analysis.test.test_basic/output.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

and the final error:

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Standard error
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
analysis.py:79: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.
  a, b = np.linalg.lstsq(dm, ev)[0]
analysis.py:97: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.
  a, b, c = np.linalg.lstsq(dm, ev)[0]
/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/blav.py:93: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.
  error, b = np.linalg.lstsq(dm, ev)[0]
Traceback (most recent call last):
  File "analysis.py", line 68, in <module>
    spectrum = Spectrum(f, start=nskip, path='trajectory/press', bsize=len(press)-nskip)
  File "/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/spectrum.py", line 126, in __init__
    AnalysisHook.__init__(self, f, start, end, None, step, analysis_inputs, outpath, True)
  File "/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/hook.py", line 104, in __init__
    self.compute_offline()
  File "/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/hook.py", line 138, in compute_offline
    self.init_first()
  File "/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/spectrum.py", line 179, in init_first
    AnalysisHook.init_first(self)
  File "/dev/shm/build/yaff/1.6.0/foss-2020b/yaff-1.6.0/yaff/analysis/hook.py", line 150, in init_first
    self.outg = self.f.create_group(self.outpath)
  File "/home/apps/USE/easybuild/staging/2021.1/software/h5py/3.1.0-foss-2020b/lib/python3.8/site-packages/h5py/_hl/group.py", line 65, in create_group
    gid = h5g.create(self.id, name, lcpl=lcpl, gcpl=gcpl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5g.pyx", line 162, in h5py.h5g.create
ValueError: Unable to create group (no write intent on file)
Traceback (most recent call last):
  File "runall.py", line 32, in <module>
    subprocess.check_call(["python", "analysis.py", "300", "310", "10"], cwd='nvt')
  File "/home/apps/USE/easybuild/staging/2021.1/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/subprocess.py", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['python', 'analysis.py', '300', '310', '10']' returned non-zero exit status 1.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Provide cleaner instructions for conda installation

add in your README to create a separate virtual env for yaff with:

conda create -n yaff python=x.x 
conda install gcc_linux-64 gxx_linux-64 gfortran_linux-64
conda install -c molmol yaff

error: there are 6 tasks failed when I run the tests.

Hi,

When I tested Yaff, 6 of them failed.

The errors were attached below:
check_example() takes 3 positional arguments but 4 were given and No module named 'yaff.yaff.version'

Thanks!

HDF5 version > 1.10 not working

Dear maintainers,

I am part of the EasyBuild community and I am trying to build YAFF-1.6.0 with HDF5 version 1.12.x. Due to a change of the API that build is failing.
As we want to use YAFF for testing LAMMPS (see PR #15869 and for dependency reasons we got HDF5-1.12.x in our toolchain, it would be highly desirable to look into that and make the software compatible with newer versions of HDF5.

Please let me know if you require any further information.

Thanks for your help, much appreciated!

Units of MM3 covalent terms

There is some confusion about the implementation of the MM3Quartic and MM3Bend ValenceTerms in Yaff. The expression for the MM3Quartic term for example looks like this:

0.5K(q-q0)^2*(1-2.55*(q-q0)+7/12*(2.55*(q-q0))^2)

The constant 2.55 has a dimension of [1/length] and thus depends on the internal units used. The original paper is not clear whether 2.55 is the value in angstrom^-1 or in bohr^-1. Here it is mentioned that 2.55 is the value in angstrom^-1. This is confirmed by the implementation in pydlpoly.
If this is correct, the Yaff implementation needs to be changed. Because Yaff uses atomic units, 2.55 has to be expressed in bohr^-1.

Python 3.8 compatibility

During the preparation of migrating to python 3.8 we noticed that the yaff package still uses time.clock which is no longer available in Python 3.8 please use time.process_time instead.
conda-forge/yaff-feedstock#4

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.