pylada / pylada-light

A physics computational framework for python and ipython

pylada-crystal

A python computational physics framework.

Minimal version of pylada necessary to just run the crystal,VASP,ewald,jobs,and database modules

Constructed by Peter Graf from Mayeul d'Avezac's pylada

Usage

There are some IPython notebooks in the notebooks subdirectory. And documentation can be found [online](http://pylada.github.io/pylada-light/), though somewhat out of date. Notably, it does not describe the PWSCF wrapper.

For more examples, look at the tests in each subfolder, and at the BDD scenarios in the espresso/tests/bdd/features folder.

Finally, do join us on [slack](pylada.slack.com). Send one of the authors an email if you need access.

Installation

The simplest approach is to install via pip:

• global installation

  pip install git+https://github.com/pylada/pylada-light

• local (user) installation

  pip install --user git+https://github.com/pylada/pylada-light

• in a virtual environment

  python -m venv pylada
  source pylada/bin/activate
  pip install git+https://github.com/pylada/pylada-light

  This last approach is recommended since it keeps the pylada environment isolated from the rest of the system. Susbsequently, this environment can be accessed by running the second line.

Installation for development

• python setup.py develop

  python -m venv pylada
  source pylada/bin/activate
  git clone https://github.com/pylada/pylada-light
  cd pylada-light
  python -m pip install cython setuptools wheel scikit-build cmake ninja numpy
  python -m pip install -e .[dev]
  python setup.py test
  ln -s src/pylada . # because https://github.com/scikit-build/scikit-build/issues/363

  The above creates a virtual environment and installs pylada inside it in development mode. This means that the virtual environment will know about the pylada flavor in development. It is possible to edit a file, do make, launch python and debug. One just needs to active the virtual environment once per session.

  When modifying files that are built (.pyx, .cc, .h), it may be necessary to run python setup.py develop again.

pylada-light's Issues

gmake (cmake) error.

Hello. I faced the problem of gmake error. My local have two cmake version (cmake, cmake3). So I modify setup.py as cmake = find_executable('cmake3'). The cmake3 's version is 3.12.1 and then I did 'python setup.py install'. Below is the error.

[ 54%] Built target pylada.crystal
[ 57%] Building CXX object crystal/defects/CMakeFiles/third_order.dir/third_order.cc.o
/home/woohyun/9_program/pylada_light_python2/pylada-light-master/crystal/defects/third_order.cc: In function ‘pylada::types::t_real pylada::third_order(const Eigen::MatrixBase&, pylada::types::t_int)’:
/home/woohyun/9_program/pylada_light_python2/pylada-light-master/crystal/defects/third_order.cc:43:26: error: ‘v’ does not name a type
auto const v = rVector3d(i * ninv + l - 0.5, j * ninv + m - 0.5, k * ninv + n - 0.5);
^
/home/woohyun/9_program/pylada_light_python2/pylada-light-master/crystal/defects/third_order.cc:44:43: error: ‘v’ was not declared in this scope
t_real const q = (_matrix * v).squaredNorm();
^
/home/woohyun/9_program/pylada_light_python2/pylada-light-master/crystal/defects/third_order.cc: In function ‘pylada::types::t_real pylada::third_order(const t_real*, pylada::types::t_int)’:
/home/woohyun/9_program/pylada_light_python2/pylada-light-master/crystal/defects/third_order.cc:56:14: error: ‘matrix’ does not name a type
auto const matrix = types::rMatrix3d::Map(_matrix).transpose();
^
/home/woohyun/9_program/pylada_light_python2/pylada-light-master/crystal/defects/third_order.cc:57:22: error: ‘matrix’ was not declared in this scope
return third_order(matrix, _n);
^
gmake[2]: *** [crystal/defects/CMakeFiles/third_order.dir/third_order.cc.o] error 1
gmake[1]: *** [crystal/defects/CMakeFiles/third_order.dir/all] error 2
gmake: *** [all] error 2
error: command '/usr/bin/cmake3' failed with exit status 2

primitive leads to: pylada.error.RuntimeError: Size and volumes do not match.

Using the primitive functions when the structure is not primitive leads to the error stated in the title. For example:

With the following structure (POSCAR_Si)

cubic diamond
   5.43
 1.0    0.0     0.0
 0.0    1.0     0.0
 0.0    0.0     1.0
 Si
 8
Direct
 -0.125 -0.125 -0.125
 -0.125  0.375  0.375
  0.375 -0.125  0.375
  0.375  0.375 -0.125
  0.125  0.125  0.125
  0.125  0.625  0.625
  0.625  0.125  0.625
  0.625  0.625  0.125

I run:

python -c "from pylada.crystal import read, primitive; primitive(read.poscar(\"POSCAR_Si\"))"

and I get:

03/15/2023 11:49:08 PM Size and volumes do not match.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "_primitive.pyx", line 152, in pylada.crystal._primitive.primitive
pylada.error.RuntimeError: Size and volumes do not match.

This was not the case for a version of pylada installed in Jan 2022.

Error in third_order.cc

I got the following error while installing pylada:

[ 57%] Building CXX object crystal/defects/CMakeFiles/third_order.dir/third_order.cc.o
/tmp/pip-req-build-bs7_xdv1/crystal/defects/third_order.cc: In function ‘pylada::types::t_real pylada::third_order(const Eigen::MatrixBase&, pylada::types::t_int)’:
/tmp/pip-req-build-bs7_xdv1/crystal/defects/third_order.cc:43:26: error: ‘v’ does not name a type
auto const v = rVector3d(i * ninv + l - 0.5, j * ninv + m - 0.5, k * ninv + n - 0.5);

Pylada-light installation error

Hi I am trying to install pylada-light

When I entered pip3 install git+https://github.com/pylada/pylada-light --user,
an error appeared below.

Installing collected packages: pylada
Running setup.py install for pylada: started
Running setup.py install for pylada: finished with status 'error'
CMake Warning (dev) at build/external/src/GreatCMakeCookOff/cmake/GreatCMakeCookOffConfig.cmake:6 (set):
implicitly converting 'DOC' to 'STRING' type.
Call Stack (most recent call first):
cmake_modules/LookUp-GreatCMakeCookOff.cmake:13 (find_package)
CMakeLists.txt:31 (include)
This warning is for project developers. Use -Wno-dev to suppress it.

-- Found Eigen3
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/pip-req-build-mg7bw46u/build
CMake: building in /tmp/pip-req-build-mg7bw46u/build
/home/jaehyeon/opt/cmake-3.16.2/bin/cmake --build /tmp/pip-req-build-mg7bw46u/build
[  0%] Built target lookup_dependencies
[  0%] Built target pylada_error
[  8%] Built target pylada.crystal._map_sites-cython
[ 20%] Built target cutilities
[ 28%] Built target pylada.crystal.cutilities-cython
[ 37%] Built target pylada.crystal._primitive-cython
[ 45%] Built target pylada.crystal._coordination_shells-cython
[ 54%] Built target pylada.crystal._space_group-cython
[ 54%] Built target pylada.crystal
[ 57%] Building CXX object crystal/defects/CMakeFiles/third_order.dir/third_order.cc.o
/tmp/pip-req-build-mg7bw46u/crystal/defects/third_order.cc: In function ‘pylada::types::t_real pylada::third_order(const Eigen::MatrixBase<Derived>&, pylada::types::t_int)’:
/tmp/pip-req-build-mg7bw46u/crystal/defects/third_order.cc:43:26: error: ‘v’ does not name a type
               auto const v = rVector3d(i * ninv + l - 0.5, j * ninv + m - 0.5, k * ninv + n - 0.5);
                          ^
/tmp/pip-req-build-mg7bw46u/crystal/defects/third_order.cc:44:43: error: ‘v’ was not declared in this scope
               t_real const q = (_matrix * v).squaredNorm();
                                           ^
/tmp/pip-req-build-mg7bw46u/crystal/defects/third_order.cc: In function ‘pylada::types::t_real pylada::third_order(const t_real*, pylada::types::t_int)’:
/tmp/pip-req-build-mg7bw46u/crystal/defects/third_order.cc:56:14: error: ‘matrix’ does not name a type
   auto const matrix = types::rMatrix3d::Map(_matrix).transpose();
              ^
/tmp/pip-req-build-mg7bw46u/crystal/defects/third_order.cc:57:22: error: ‘matrix’ was not declared in this scope
   return third_order(matrix, _n);
                      ^
gmake[2]: *** [crystal/defects/CMakeFiles/third_order.dir/third_order.cc.o] Error 1
gmake[1]: *** [crystal/defects/CMakeFiles/third_order.dir/all] Error 2
gmake: *** [all] Error 2
error: command '/home/jaehyeon/opt/cmake-3.16.2/bin/cmake' failed with exit status 2
----------------------------------------

ERROR: Command "/TGM/Apps/PYTHON/3.6.6_ICC18.0.3/bin/python3.6 -u -c 'import setuptools, tokenize;file='"'"'/tmp/pip-req-build-mg7bw46u/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-vze59oc4/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-req-build-mg7bw46u/

May I ask you solution for this error??

My python version: 3.6.6
cmake version: 3.16.2

Python 3.6 compatibility problem

I tried to install pylada via pip on different machines (Mac and CentOS). On both of them installed python3.6.
For both cases I got:

    [ 37%] Building CXX object crystal/CMakeFiles/cutilities.dir/smith_normal_form.cc.o
    In file included from /private/var/folders/kw/ctt8d34s3cs6y_pg9nq3p3mrbjlb91/T/pip-t4402nwy-build/crystal/smith_normal_form.cc:26:
    In file included from /private/var/folders/kw/ctt8d34s3cs6y_pg9nq3p3mrbjlb91/T/pip-t4402nwy-build/crystal/cutilities.h:4:
    In file included from /private/var/folders/kw/ctt8d34s3cs6y_pg9nq3p3mrbjlb91/T/pip-t4402nwy-build/crystal/types.h:29:
    /usr/local/include/eigen3/Eigen/Core:273:10: fatal error: 'type_traits' file not found
    #include <type_traits>
             ^~~~~~~~~~~~~
    1 error generated.
    make[2]: *** [crystal/CMakeFiles/cutilities.dir/smith_normal_form.cc.o] Error 1
    make[1]: *** [crystal/CMakeFiles/cutilities.dir/all] Error 2
    make: *** [all] Error 2
    error: command '/usr/local/bin/cmake' failed with exit status 2

Any ideas what can be wrong?

%launch scattered fails with new version of pylada (after June 2018)

We get the following error when launching jobs with:

%launch scattered --account=NRELMatDB --walltime=48:00:00 --ppn=24 --queue=batch-h --feature=haswell --nbprocs=48

Error message:

/home/pgorai/.conda-envs/prashun/lib/python2.7/site-packages/pylada/ipython/launch/scattered.pyc in launch(self, event, jobfolders)
     47     from ... import pbs_string, default_pbs, qsub_exe, default_comm
     48     from . import get_walltime, get_mppalloc, get_queues, scattered_script
---> 49     from .. import logger, Pylada
     50
     51     if not hasattr(pylada, 'ipython_qstat'):

ImportError: cannot import name Pylada

Reverting to may 30th commit (Bug fix in the logger for the mpi hostfile) the error does not occur. Any idea what this could be?

About KSPACING paremeter in INCAR

Can I use "KSPACING" parameter in "INCAR"? I found that vasp function writes KPOINTS file in the directory. How do I block it in order to use "KSPACING" parameter in "INCAR"

determine hostnames from PBS_NODEFILE, SLURM_NODEFILE, SLURM_NODELIST

Rather than use mpi4py

Using Decorations to Enumerate Alloy Configurations

Hello! I'm a grad student in Vladan's group. I've been doing some work with alloys and was looking at the following code: pylada-light/tests/decorations/test_generator.py. I know this code was written a while ago, but if you do happen to remember a few things about it, I'd greatly appreciate some help.

I was using this code to produce all symmetry inequivalent structures for an FCC lattice with a supercell size of 2.
In the results list in that code, I get something like:
['101002 01', '101012 01']. Am I right in assuming that the first number is the transformation matrix (or Hermite Normal Form Matrix) and the second is the decoration?

Second, is it possible to obtain the degeneracy of each of these configurations? For instance, if I were to produce all possible decorations and supercells for an n=2 FCC supercell, would it be possible to figure out how many of the results correspond to the first structure versus the second?

Thanks for your help!
Drew

Hostfile does not work with openmpi

pylada-light/process/mpi.py

Lines 177 to 179 in 7e78d8f

	##file.write('{0} slots={1}\n'.format(machine, slots))
	file.write(machine)
	file.write('\n')

The default behavior of mpirun in openmpi is to assume 1 slot(core) per host, which makes any call to mpirun fail when more than one core is used. This can be solved by uncommenting L177 and removing L178-L179.

Why was it commented in the first place? The current version works with intel mpi, but uncommenting L177 works with both intel mpi and openmpi so why loose the generality by commenting it?

Also, on the bigger picture, what is the advantage of writing the hostfile? The job scheduler writes it automatically if it is not specified. As much as I can tell, not having to check the hosts manually would free pylada from the mpi4py depdendency.

DFT+U Broken without NLEP

I use DFT+U without the NLEP modified code and noticed that the INCAR is written incorrectly for the vasp U parameters. The following patch file fixed my problems when applied to the vasp/keywords.py file. I haven't done any testing with the nlep code so I am not sure how that will interact.

1040c1040
<             ldul, lduu, lduj = [], [], []
---
>             ldaul, ldauu, ldauj = [], [], []
1052,1057c1052,1057
<                 ldul.append('{0[0]}'.format(a))
<                 lduu.append('{0[1]:18.10e}'.format(a))
<                 lduj.append('{0[2]:18.10e}'.format(a))
<             result['LDUL'] = ' '.join(ldul)
<             result['LDUU'] = ' '.join(lduu)
<             result['LDUJ'] = ' '.join(lduj)
---
>                 ldaul.append('{0[0]}'.format(a))
>                 ldauu.append('{0[1]:18.10e}'.format(a))
>                 ldauj.append('{0[2]:18.10e}'.format(a))
>             result['LDAUL'] = ' '.join(ldaul)
>             result['LDAUU'] = ' '.join(ldauu)
>             result['LDAUJ'] = ' '.join(ldauj)

keywords.patch.txt

travis failing because.... travis?

ModuleNotFoundError: No module named 'py'

When I install pylada in an empy envrionment I get the following error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/felixt/.conda-envs/testcw/lib/python3.8/site-packages/pylada/__init__.py", line 121, in <module>
    logger = __setup_logger()
  File "/home/felixt/.conda-envs/testcw/lib/python3.8/site-packages/pylada/__init__.py", line 100, in __setup_logger
    local_dict = __exec_config_files("logging.py")
  File "/home/felixt/.conda-envs/testcw/lib/python3.8/site-packages/pylada/__init__.py", line 87, in __exec_config_files
    for filename in __find_config_files(pattern, rcfile):
  File "/home/felixt/.conda-envs/testcw/lib/python3.8/site-packages/pylada/__init__.py", line 68, in __find_config_files
    from py.path import local
ModuleNotFoundError: No module named 'py'

This is a new error because "py" used to be installed as a dependency for "pytest" but it seems like it is no longer installed since pytest is required only for tests (tests_require).

We could maybe add "py" to install_requires or not use py.path whatsoever and use "os" instead? @mdavezac, what do you think?

[DUPE] Some tests fail when testsuite run in travis-ci

Hi -- I'm trying to build a conda package for pylada with some CI to build the package, run the testsuite, update my anaconda channel with the build artifact for macOS and linux.

Some of the tests in the testsuite fail when run on travis-ci -- the testsuite work's fine when run on my machine locally -- but same set of tests fail on macOS and linux when run in CI. I think that possibly the failure might have something to do with openmp -- but not really sure ... Thought I could ask and see if someone already knows the issue and possibly a fix? These are the tests that fail:

Total Test time (real) = 335.44 sec
The following tests FAILED:
	  6 - pylada.crystal.map_sites (Failed)
	 61 - pifunctional (Failed)
	 62 - pylada.process.call (Failed)
	 63 - pylada.process.iterator (Failed)
	 64 - pylada.process.program (Failed)
	 65 - pylada.process.jobfolder (Failed)
	 82 - pylada.notebooks.notebooks (Failed)

I'm attaching the full raw.log from one of the travis-ci job's -- the full output of ctest -V is near the end of file...

Many thanks!

Python 3.5, Linux, package problem

Hi!

I just tried to compile pylada-light on my laptop with Ubuntu 16.04, Python 3.5.2. I switched into python3 branch.
Then I have built it myself and it finished successfully. But my python3 could not recognize pylada as a package. That's why I have copied pylada directory from pylada_package into a necessary directory with all packages by hands.
That means that it does not copy it themselves.
Is it a common problem or just I am an only person, who faced it?

Segmentation Error

In continuation of unresolved issues specified in #28, after compilation of the pylada package, on attempt to import pylada, even after a fresh compilation using the suggested CXXFLAGS=-std=c++11, I am met with a segmentation fault as follows:

(py3) hms2:~ hms2$ python
Python 3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 14:01:38)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
import faulthandler
faulthandler.enable()
import pylada
Fatal Python error: Segmentation fault
Current thread 0x00007fff8f4c0380 (most recent call first):
File "", line 219 in _call_with_frames_removed
File "", line 922 in create_module
File "", line 571 in module_from_spec
File "", line 658 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "/Users/hms2/bin/pylada-light-master/pkg_install/pylada/crystal/init.py", line 32 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "", line 219 in _call_with_frames_removed
File "", line 1023 in _handle_fromlist
File "/Users/hms2/bin/pylada-light-master/pkg_install/pylada/init.py", line 131 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "", line 1 in
Segmentation fault: 11

Syntax error when importing pylada

I get a syntax error when I import pylada. This causes an error in p2ptrans as well reported here: ftherrien/p2ptrans#31

>>> import pylada
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/felixt/p3.9/lib64/python3.9/site-packages/pylada/__init__.py", line 127, in <module>
    from . import error, crystal, physics, misc, tools, ewald, decorations, periodic_table, vasp, \
  File "/home/felixt/p3.9/lib64/python3.9/site-packages/pylada/espresso/__init__.py", line 35, in <module>
    from .structure_handling import read_structure
  File "/home/felixt/p3.9/lib64/python3.9/site-packages/pylada/espresso/structure_handling.py", line 240
    %(atom.type, atom.pos[0],atom.pos[1], atom.pos[2],
    ^
SyntaxError: invalid syntax

The "%(" should be on the previous line.

@vstevano this is from your last commits on the espresso stuff, do you not get this error?

restart from contcar on specific error

situation of vasp relaxation, which terminated with

ZBRENT: fatal error in bracketing
please rerun with smaller EDIFF, or copy CONTCAR
to POSCAR and continue"

in the stdout file.

In this case, can we let the vasp restart from the CONTCAR again and again until other error or the final success?

add binder

https://mybinder.readthedocs.io/en/latest/index.html

Writing in nodefile

pylada-light/config/mpi.py

Lines 75 to 76 in 7e78d8f

	fin.write("config/mpi: machine_dep_call_mod: nodefile contents: \"%s\"" %
	fin.read())

It seems like this line should be writing elsewhere. In the previous commit it was writing directly in the standard output. Should it be writing in the logger now? Writing this in the nodefile itself makes the %launch function fail.

Vasp top copy set of files prior to commit

This is a feature request by Xingang.
It is needed to do van der Walls and copy the vdw_bin.something file.

Pmpaths

Hi expert,

It seems I have installed pylada in Python 3.9.8. But I cannot use "from pathfinder.pmpaths import main".

Thank you very much
Jian

single cmake file without hard-coded paths

It is generally a bad idea to have hard code paths and/or multiple cmake files.
Instead, we could add a file, say "$HOME/.cmake/variables.cmake" that is included at the beginning of CMakeLists.txt, eg

if(EXISTS "$ENV{HOME}/.cmake/variables.cmake")
    include("$ENV{HOME}/.cmake/variables.cmake")
endif()

That file would have all the set(PYTHON_LIBRARIES something) needed for any particular system and user.

would that work for you, @pgraf? I can add it to the code, if it's an ok solution.

Pylada-light running problem, Python 3.9

Hello,

I installed pylada by using pip and made all of the configurations. When I try to run my script, I received an error about magic commands. The script only creates pickle file. It does not create defects folder and it is not running.

(1) If the last line of my script is given below, I got the following error.

%load_ext pylada
%savefolders defects.pickle jobfolder
%explore defects.pickle
%launch scattered

---

TypeError                                 Traceback (most recent call last)
~/pylada-work/camg2bi2/HT_defects_CaMg2Bi2.ipy in <module>
    291 get_ipython().run_line_magic('explore', 'defects.pickle')
    292 #%launch scattered --account=XXXXXX --walltime=XX:XX:XX --ppn=XX --queue=XXXXX
--> 293 get_ipython().run_line_magic('launch', 'scattered')
    294 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
   2346                 kwargs['local_ns'] = self.get_local_scope(stack_depth)
   2347             with self.builtin_trap:
-> 2348                 result = fn(*args, **kwargs)
   2349             return result
   2350 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/decorator.py in fun(*args, **kw)
    230             if not kwsyntax:
    231                 args, kw = fix(args, kw, sig)
--> 232             return caller(func, *(extras + args), **kw)
    233     fun.__name__ = func.__name__
    234     fun.__doc__ = func.__doc__

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/magics.py in launch(self, line)
     66     def launch(self, line):
     67         from .launch import launch
---> 68         return launch(self, line)
     69 
     70     @line_magic

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/launch/__init__.py in launch(self, event)
    121 
    122     # calls specialized function.
--> 123     args.func(self, args, jobfolders)
    124 
    125 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/launch/scattered.py in launch(self, event, jobfolders)
    110             # added by Peter Graf
    111             # avoid jobfolder which is already in the queue:
--> 112             qstuff = qstat(name)
    113             if (len(qstuff) > 0 and not event.force):
    114                 status = [x.split()[2] for x in qstuff]

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/launch/scattered.py in <lambda>(x)
     53         qstat = lambda x: []
     54     else:
---> 55         qstat = lambda x: self.qstat(x)
     56 
     57     logger.info("launch/scattered: event: %s" % event)

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/decorator.py in fun(*args, **kw)
    230             if not kwsyntax:
    231                 args, kw = fix(args, kw, sig)
--> 232             return caller(func, *(extras + args), **kw)
    233     fun.__name__ = func.__name__
    234     fun.__doc__ = func.__doc__

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/magics.py in qstat(self, arg)
    116             return None
    117 
--> 118         result = ipython_qstat(self, arg)
    119         if len(arg) == 0:
    120             return result

~/.pylada in ipython_qstat(self, arg)
     19   # get user jobs ids
     20 
---> 21   jobs   = Popen(['squeue', '-u', 'ksevim'], stdout=PIPE)   \
     22                 .communicate()[0].split('\n')
     23 

TypeError: a bytes-like object is required, not 'str'
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-7-2bdefd50f77d> in <module>
----> 1 get_ipython().run_line_magic('run', './HT_defects_CaMg2Bi2.ipy')

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
   2346                 kwargs['local_ns'] = self.get_local_scope(stack_depth)
   2347             with self.builtin_trap:
-> 2348                 result = fn(*args, **kwargs)
   2349             return result
   2350 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/decorator.py in fun(*args, **kw)
    230             if not kwsyntax:
    231                 args, kw = fix(args, kw, sig)
--> 232             return caller(func, *(extras + args), **kw)
    233     fun.__name__ = func.__name__
    234     fun.__doc__ = func.__doc__

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/magics/execution.py in run(self, parameter_s, runner, file_finder)
    722             with preserve_keys(self.shell.user_ns, '__file__'):
    723                 self.shell.user_ns['__file__'] = filename
--> 724                 self.shell.safe_execfile_ipy(filename, raise_exceptions=True)
    725             return
    726 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/interactiveshell.py in safe_execfile_ipy(self, fname, shell_futures, raise_exceptions)
   2833                     result = self.run_cell(cell, silent=True, shell_futures=shell_futures)
   2834                     if raise_exceptions:
-> 2835                         result.raise_error()
   2836                     elif not result.success:
   2837                         break

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/interactiveshell.py in raise_error(self)
    329             raise self.error_before_exec
    330         if self.error_in_exec is not None:
--> 331             raise self.error_in_exec
    332 
    333     def __repr__(self):

    [... skipping hidden 1 frame]

<ipython-input-7-b0cf0817cb8e> in <module>
    291 get_ipython().run_line_magic('explore', 'defects.pickle')
    292 #%launch scattered --account=XXXXXX --walltime=XX:XX:XX --ppn=XX --queue=XXXXX
--> 293 get_ipython().run_line_magic('launch', 'scattered')
    294 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
   2346                 kwargs['local_ns'] = self.get_local_scope(stack_depth)
   2347             with self.builtin_trap:
-> 2348                 result = fn(*args, **kwargs)
   2349             return result
   2350 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/decorator.py in fun(*args, **kw)
    230             if not kwsyntax:
    231                 args, kw = fix(args, kw, sig)
--> 232             return caller(func, *(extras + args), **kw)
    233     fun.__name__ = func.__name__
    234     fun.__doc__ = func.__doc__

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/magics.py in launch(self, line)
     66     def launch(self, line):
     67         from .launch import launch
---> 68         return launch(self, line)
     69 
     70     @line_magic

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/launch/__init__.py in launch(self, event)
    121 
    122     # calls specialized function.
--> 123     args.func(self, args, jobfolders)
    124 
    125 

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/launch/scattered.py in launch(self, event, jobfolders)
    110             # added by Peter Graf
    111             # avoid jobfolder which is already in the queue:
--> 112             qstuff = qstat(name)
    113             if (len(qstuff) > 0 and not event.force):
    114                 status = [x.split()[2] for x in qstuff]

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/launch/scattered.py in <lambda>(x)
     53         qstat = lambda x: []
     54     else:
---> 55         qstat = lambda x: self.qstat(x)
     56 
     57     logger.info("launch/scattered: event: %s" % event)

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/decorator.py in fun(*args, **kw)
    230             if not kwsyntax:
    231                 args, kw = fix(args, kw, sig)
--> 232             return caller(func, *(extras + args), **kw)
    233     fun.__name__ = func.__name__
    234     fun.__doc__ = func.__doc__

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

~/anaconda3/envs/pylada3/lib/python3.9/site-packages/pylada/ipython/magics.py in qstat(self, arg)
    116             return None
    117 
--> 118         result = ipython_qstat(self, arg)
    119         if len(arg) == 0:
    120             return result

~/.pylada in ipython_qstat(self, arg)
     19   # get user jobs ids
     20 
---> 21   jobs   = Popen(['squeue', '-u', 'ksevim'], stdout=PIPE)   \
     22                 .communicate()[0].split('\n')
     23 

TypeError: a bytes-like object is required, not 'str'

---

(2) If the last line of my script is given below, I did not get any error message. I had only pickle file saved into working directory and nothing is running.

if '__IPYTHON__' in globals():
ipython.magic('load_ext pylada')
ipython.magic('savefolders defects.pkl jobfolder')
ipython.magic('explore defects.pkl')
ipython.magic('launch scattered')

I also tried to use get_ipython().run_line_magic('launch', 'scattered') in my script but I got the same error in (1).

Could you please help me to run my script in python 3 environment. What should I use to run magic commands in python 3?

Best Regards,
Koray

Installation fails when mpi4py is unavailable

Hello!

I have ptyhon3.7 and tried to compile pylada on my Mac.
I ran python3 setup.py install and it gives me finally an error:

error: package directory 'build/pylada/process/tests' does not exist

Then I tried to compile it by hands and made and everything is fine until I am importing pylada inside python3 it says follows:

>>> import pylada
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'pylada'

Then I checked site-packages folder and I did not find pylada directory there.

What can be wrong with it?

ImportError: libgfortran.so

I install pylada with my own library and cmake because of no permission.

  File "/vol6/home/****/anaconda3/lib/python3.7/site-packages/py_vasp-1.5.3-py3.7.egg/py_vasp/exstructure.py", line 1, in <module>
    from pylada.crystal.structure import Structure
  File "/vol6/home/****/anaconda3/lib/python3.7/site-packages/pylada/__init__.py", line 131, in <module>
    from . import error, crystal, physics, misc, tools, ewald, decorations, periodic_table, vasp, \
ImportError: libgfortran.so.3: cannot open shared object file: No such file or directory
yhrun: error: cn1510: tasks 12-23: Exited with exit code 1
(base) [****@***** root_dir]$ python -c "from pylada.crystal.structure import Structure"
(base) [****@***** root_dir]$

Environment
gcc-7.3.0
cmake-3.15
anaconda3

Tests failing after PR #67

Some tests are failing since PR #67 (or before?!)

================================== short test summary info ===================================
FAILED tests/decorations/test_defects.py::test_iterator - AttributeError: 'pylada.decorations._decorations.FCIterator' object has no attribute '_FC...
FAILED tests/decorations/test_fciterator.py::test_fciterator - AttributeError: 'pylada.decorations._decorations.FCIterator' object has no attribute '_FC...
FAILED tests/espresso/test_extract.py::test_cellshape - AssertionError: assert False
FAILED tests/espresso/test_pwscf.py::test_iteration - TypeError: __init__() got an unexpected keyword argument 'prefix'
FAILED tests/espresso/bdd/test_restart.py::test_check_restart_input - pylada.error.RuntimeError: Cannot restart from unsuccessful calculation
FAILED tests/espresso/bdd/test_restart.py::test_check_restarted_run - pylada.error.RuntimeError: Cannot restart from unsuccessful calculation
============= 6 failed, 475 passed, 35 skipped, 58 warnings in 74.74s (0:01:14) ==============

collections.abc in python2

A lot of us are still using python 2 (even though life is short...) and abc is still in collections for that version of the standard library such that import pylada fails with:

from collections.abc import MutableSequence
ImportError: No module named abc

This is after 09ce322. Maybe do something like:

try:
    from collections.abc import MutableSequence
except ImportError:
    from collections import MutableSequence

That would get rid of the deprecation warning.

travis not failing when it should

It looks like errors do not get propagated from docker

Incorrect original norm in into_voronoi

Hi Mayeul,

I was using the into_voronoi routine in another context, and found an error.

def into_voronoi(position, cell, inverse=None):

    from numpy import dot, floor
    from numpy.linalg import inv, norm
    if inverse is None:
        inverse = inv(cell)
    center = dot(inverse, position)
    center -= floor(center)
    result = center
    n = norm(center)
    for i in range(-1, 2, 1):
        for j in range(-1, 2, 1):
            for k in range(-1, 2, 1):
                translated = [i, j, k] + center
                n2 = norm(dot(cell, translated))
                if n2 < n:
                    n = n2
                    result = translated
    return dot(cell, result)


n = norm(center) should be  n = norm(dot(cell,center))

In analogy to n2 = norm(dot(cell, translated))
to which it is later compared.

Restarting from previous run, order of atoms in potcar is incorrect

I noticed strange behavior when reading in results from a Relax() run to start a Vasp() run.
The order of the POTCAR rearranged, but the structure file stayed constant -- leading to atoms 
being in the wrong positions.  

I tried to identify the source of the error to no avail.  However, I was able to remedy the error by
using Relax() instead of Vasp() for the second run, then manually changing the settings to what
I needed (e.g. Relax().relaxation='static').

Installation does not work with icc and ifort

While we are at it, this is another issue we came accross while installing pylada on the new system. Pylada installs smoothly with gcc and gfortran, but when trying to install it using ifort and icc (i.e. they are the default compiler found by cmake when the intel modules are loaded) we get the following error:

/home/felixt/src/pylada-impi/ewald/erfc.cc(26): error: identifier "std_erfc" is undefined

      extern "C" double FC_GLOBAL_(std_erfc, STD_ERFC)( const double *const _in )
                                   ^
    /home/felixt/src/pylada-impi/ewald/erfc.cc(26): error: expected a ")"

      extern "C" double FC_GLOBAL_(std_erfc, STD_ERFC)( const double *const _in )
                                           ^
    /home/felixt/src/pylada-impi/ewald/erfc.cc(26): error: expected a ";"

      extern "C" double FC_GLOBAL_(std_erfc, STD_ERFC)( const double *const _in )
                                                      ^
    compilation aborted for /home/felixt/src/pylada-impi/ewald/erfc.cc (code 2)

This is because FC_GLOBAL (and FC_MODULE) is not defined in build/FCMangle.h as it should. This happens when Cmake is unable to interface C and Fortran. One way to check this is to add:

FortranCInterface_VERIFY()

in CMakeLists.txt. After doing so, we get the following error:

Call Stack (most recent call first):

     /home/felixt/.conda-envs/testenv/share/cmake-3.11/Modules/FortranCInterface/Verify/CMakeLists.txt:16 (FortranCInterface_HEADER)

    This warning is for project developers.  Use -Wno-dev to suppress it.

    -- Verifying Fortran/C Compiler Compatibility - Failed

    CMake Error at /home/felixt/.conda-envs/testenv/share/cmake-3.11/Modules/FortranCInterface.cmake:383 (message):

      The Fortran compiler:

        /nopt/intel/psxe2017u2/compilers_and_libraries_2017.5.239/linux/bin/intel64/ifort

      and the C compiler:

        /nopt/intel/psxe2017u2/compilers_and_libraries_2017.5.239/linux/bin/intel64/icc

      failed to compile a simple test project using both languages.

I am not sure how to proceed to solve this error... It might be independant of pylada...

Segfault when running primitive on specific structure

It doesn’t always give primitive of the supercell. If I reduce tolerance below symprec = 1e-8, the function crashes with
segmentation fault. For example
sc = Structure( 16.7408, 8.37309, 4.19433,
0, 14.4964, 2.42101,
0, 0, 20.2397,
scale=1 )
.add_atom(4.18631, 2.41645, 1.95011, ‘Bi’)
.add_atom(6.28347, 3.62695, 12.07, ‘Bi’)
.add_atom(6.27958, 6.04054, 1.95011, ‘Bi’)
.add_atom(8.37674, 7.25105, 12.07, ‘Bi’)
.add_atom(8.37285, 9.66464, 1.95011, ‘Bi’)
.add_atom(10.47, 10.8751, 12.07, ‘Bi’)
.add_atom(10.4661, 13.2887, 1.95011, ‘Bi’)
.add_atom(12.5633, 14.4992, 12.07, ‘Bi’)
.add_atom(8.3715, 2.41645, 1.95011, ‘Bi’)
.add_atom(10.4687, 3.62695, 12.07, ‘Bi’)
.add_atom(10.4648, 6.04055, 1.95011, ‘Bi’)
.add_atom(12.5619, 7.25105, 12.07, ‘Bi’)
.add_atom(12.558, 9.66464, 1.95011, ‘Bi’)
.add_atom(14.6552, 10.8751, 12.07, ‘Bi’)
.add_atom(14.6513, 13.2887, 1.95011, ‘Bi’)
.add_atom(16.7485, 14.4992, 12.07, ‘Bi’)
.add_atom(12.5567, 2.41645, 1.95011, ‘Bi’)
.add_atom(14.6539, 3.62695, 12.07, ‘Bi’)
.add_atom(14.65, 6.04055, 1.95011, ‘Bi’)
.add_atom(16.7471, 7.25105, 12.07, ‘Bi’)
.add_atom(16.7432, 9.66464, 1.95011, ‘Bi’)
.add_atom(18.8404, 10.8751, 12.07, ‘Bi’)
.add_atom(18.8365, 13.2887, 1.95011, ‘Bi’)
.add_atom(20.9337, 14.4992, 12.07, ‘Bi’)
.add_atom(16.7419, 2.41645, 1.95011, ‘Bi’)
.add_atom(18.839, 3.62696, 12.07, ‘Bi’)
.add_atom(18.8352, 6.04055, 1.95011, ‘Bi’)
.add_atom(20.9323, 7.25105, 12.07, ‘Bi’)
.add_atom(20.9284, 9.66464, 1.95011, ‘Bi’)
.add_atom(23.0256, 10.8751, 12.07, ‘Bi’)
.add_atom(23.0217, 13.2887, 1.95011, ‘Bi’)
.add_atom(25.1189, 14.4992, 12.07, ‘Bi’)
.add_atom(4.18932, 2.41815, 8.16974, ‘Bi’)
.add_atom(6.28648, 3.62865, 18.2896, ‘Bi’)
.add_atom(6.28259, 6.04224, 8.16974, ‘Bi’)
.add_atom(8.37975, 7.25275, 18.2896, ‘Bi’)
.add_atom(8.37586, 9.66634, 8.16974, ‘Bi’)
.add_atom(10.473, 10.8768, 18.2896, ‘Bi’)
.add_atom(10.4691, 13.2904, 8.16974, ‘Bi’)
.add_atom(12.5663, 14.5009, 18.2896, ‘Bi’)
.add_atom(8.37451, 2.41815, 8.16974, ‘Bi’)
.add_atom(10.4717, 3.62865, 18.2896, ‘Bi’)
.add_atom(10.4678, 6.04224, 8.16974, ‘Bi’)
.add_atom(12.5649, 7.25275, 18.2896, ‘Bi’)
.add_atom(12.5611, 9.66634, 8.16974, ‘Bi’)
.add_atom(14.6582, 10.8768, 18.2896, ‘Bi’)
.add_atom(14.6543, 13.2904, 8.16974, ‘Bi’)
.add_atom(16.7515, 14.5009, 18.2896, ‘Bi’)
.add_atom(12.5597, 2.41815, 8.16974, ‘Bi’)
.add_atom(14.6569, 3.62865, 18.2896, ‘Bi’)
.add_atom(14.653, 6.04224, 8.16974, ‘Bi’)
.add_atom(16.7501, 7.25275, 18.2896, ‘Bi’)
.add_atom(16.7462, 9.66634, 8.16974, ‘Bi’)
.add_atom(18.8434, 10.8768, 18.2896, ‘Bi’)
.add_atom(18.8395, 13.2904, 8.16974, ‘Bi’)
.add_atom(20.9367, 14.5009, 18.2896, ‘Bi’)
.add_atom(16.7449, 2.41815, 8.16974, ‘Bi’)
.add_atom(18.8421, 3.62865, 18.2896, ‘Bi’)
.add_atom(18.8382, 6.04224, 8.16974, ‘Bi’)
.add_atom(20.9353, 7.25275, 18.2896, ‘Bi’)
.add_atom(20.9314, 9.66634, 8.16974, ‘Bi’)
.add_atom(23.0286, 10.8768, 18.2896, ‘Bi’)
.add_atom(23.0247, 13.2904, 8.16974, ‘Bi’)
.add_atom(25.1219, 14.5009, 18.2896, ‘Bi’)
.add_atom(20.9312, 4.8346, 10.1199, ‘Se’)
.add_atom(6.2876, 6.0451, 20.2397, ‘Se’)
.add_atom(23.0245, 8.45869, 10.1199, ‘Se’)
.add_atom(8.38087, 9.6692, 20.2397, ‘Se’)
.add_atom(25.1177, 12.0828, 10.1199, ‘Se’)
.add_atom(10.4741, 13.2933, 20.2397, ‘Se’)
.add_atom(27.211, 15.7069, 10.1199, ‘Se’)
.add_atom(4.19433, 2.42101, 20.2397, ‘Se’)
.add_atom(8.37563, 4.8346, 10.1199, ‘Se’)
.add_atom(10.4728, 6.0451, 20.2397, ‘Se’)
.add_atom(10.4689, 8.45869, 10.1199, ‘Se’)
.add_atom(12.5661, 9.6692, 20.2397, ‘Se’)
.add_atom(12.5622, 12.0828, 10.1199, ‘Se’)
.add_atom(14.6593, 13.2933, 20.2397, ‘Se’)
.add_atom(14.6554, 15.7069, 10.1199, ‘Se’)
.add_atom(8.37952, 2.42101, 20.2397, ‘Se’)
.add_atom(12.5608, 4.8346, 10.1199, ‘Se’)
.add_atom(14.658, 6.0451, 20.2397, ‘Se’)
.add_atom(14.6541, 8.45869, 10.1199, ‘Se’)
.add_atom(16.7513, 9.6692, 20.2397, ‘Se’)
.add_atom(16.7474, 12.0828, 10.1199, ‘Se’)
.add_atom(18.8445, 13.2933, 20.2397, ‘Se’)
.add_atom(18.8406, 15.7069, 10.1199, ‘Se’)
.add_atom(12.5647, 2.42101, 20.2397, ‘Se’)
.add_atom(16.746, 4.8346, 10.1199, ‘Se’)
.add_atom(18.8432, 6.0451, 20.2397, ‘Se’)
.add_atom(18.8393, 8.45869, 10.1199, ‘Se’)
.add_atom(20.9364, 9.6692, 20.2397, ‘Se’)
.add_atom(20.9325, 12.0828, 10.1199, ‘Se’)
.add_atom(23.0297, 13.2933, 20.2397, ‘Se’)
.add_atom(23.0258, 15.7069, 10.1199, ‘Se’)
.add_atom(16.7499, 2.42101, 20.2397, ‘Se’)
.add_atom(6.28326, 3.62685, 6.60167, ‘Se’)
.add_atom(8.38042, 4.83735, 16.7215, ‘Se’)
.add_atom(8.37653, 7.25094, 6.60167, ‘Se’)
.add_atom(10.4737, 8.46145, 16.7215, ‘Se’)
.add_atom(10.4698, 10.875, 6.60166, ‘Se’)
.add_atom(12.567, 12.0855, 16.7215, ‘Se’)
.add_atom(12.5631, 14.4991, 6.60167, ‘Se’)
.add_atom(14.6602, 15.7096, 16.7215, ‘Se’)
.add_atom(10.4685, 3.62685, 6.60167, ‘Se’)
.add_atom(12.5656, 4.83735, 16.7215, ‘Se’)
.add_atom(12.5617, 7.25094, 6.60166, ‘Se’)
.add_atom(14.6589, 8.46144, 16.7215, ‘Se’)
.add_atom(14.655, 10.875, 6.60166, ‘Se’)
.add_atom(16.7522, 12.0855, 16.7215, ‘Se’)
.add_atom(16.7483, 14.4991, 6.60167, ‘Se’)
.add_atom(18.8454, 15.7096, 16.7215, ‘Se’)
.add_atom(14.6536, 3.62685, 6.60167, ‘Se’)
.add_atom(16.7508, 4.83735, 16.7215, ‘Se’)
.add_atom(16.7469, 7.25094, 6.60167, ‘Se’)
.add_atom(18.8441, 8.46144, 16.7215, ‘Se’)
.add_atom(18.8402, 10.875, 6.60167, ‘Se’)
.add_atom(20.9373, 12.0855, 16.7215, ‘Se’)
.add_atom(20.9335, 14.4991, 6.60167, ‘Se’)
.add_atom(23.0306, 15.7096, 16.7215, ‘Se’)
.add_atom(18.8388, 3.62685, 6.60167, ‘Se’)
.add_atom(20.936, 4.83735, 16.7215, ‘Se’)
.add_atom(20.9321, 7.25094, 6.60167, ‘Se’)
.add_atom(23.0293, 8.46144, 16.7215, ‘Se’)
.add_atom(23.0254, 10.875, 6.60167, ‘Se’)
.add_atom(25.1225, 12.0855, 16.7215, ‘Se’)
.add_atom(25.1186, 14.4991, 6.60167, ‘Se’)
.add_atom(27.2158, 15.7096, 16.7215, ‘Se’)
.add_atom(2.09236, 1.20775, 3.51819, ‘Se’)
.add_atom(4.18953, 2.41826, 13.6381, ‘Se’)
.add_atom(4.18564, 4.83185, 3.51819, ‘Se’)
.add_atom(6.2828, 6.04235, 13.6381, ‘Se’)
.add_atom(6.27891, 8.45594, 3.51819, ‘Se’)
.add_atom(8.37607, 9.66645, 13.6381, ‘Se’)
.add_atom(8.37218, 12.08, 3.51819, ‘Se’)
.add_atom(10.4693, 13.2905, 13.6381, ‘Se’)
.add_atom(6.27755, 1.20775, 3.51819, ‘Se’)
.add_atom(8.37472, 2.41826, 13.6381, ‘Se’)
.add_atom(8.37083, 4.83185, 3.51819, ‘Se’)
.add_atom(10.468, 6.04235, 13.6381, ‘Se’)
.add_atom(10.4641, 8.45594, 3.51819, ‘Se’)
.add_atom(12.5613, 9.66645, 13.6381, ‘Se’)
.add_atom(12.5574, 12.08, 3.51819, ‘Se’)
.add_atom(14.6545, 13.2905, 13.6381, ‘Se’)
.add_atom(10.4627, 1.20775, 3.51819, ‘Se’)
.add_atom(12.5599, 2.41826, 13.6381, ‘Se’)
.add_atom(12.556, 4.83185, 3.51819, ‘Se’)
.add_atom(14.6532, 6.04235, 13.6381, ‘Se’)
.add_atom(14.6493, 8.45594, 3.51819, ‘Se’)
.add_atom(16.7465, 9.66645, 13.6381, ‘Se’)
.add_atom(16.7426, 12.08, 3.51819, ‘Se’)
.add_atom(18.8397, 13.2905, 13.6381, ‘Se’)
.add_atom(14.6479, 1.20775, 3.51819, ‘Se’)
.add_atom(16.7451, 2.41826, 13.6381, ‘Se’)
.add_atom(16.7412, 4.83185, 3.51819, ‘Se’)
.add_atom(18.8384, 6.04235, 13.6381, ‘Se’)
.add_atom(18.8345, 8.45594, 3.51819, ‘Se’)
.add_atom(20.9316, 9.66645, 13.6381, ‘Se’)
.add_atom(20.9278, 12.08, 3.51819, ‘Se’)
.add_atom(23.0249, 13.2905, 13.6381, ‘Se’)
Structure( 16.7408, 8.37309, 4.19433,
0, 14.4964, 2.42101,
0, 0, 20.2397,
scale=1 )
.add_atom(12.554, -12.0799, 1.95011, ‘Bi’)
.add_atom(14.6511, -10.8694, 12.07, ‘Bi’)
.add_atom(14.6473, -8.45583, 1.95011, ‘Bi’)
.add_atom(16.7444, -7.24533, 12.07, ‘Bi’)
.add_atom(16.7405, -4.83174, 1.95011, ‘Bi’)
.add_atom(18.8377, -3.62123, 12.07, ‘Bi’)
.add_atom(2.09304, -1.20764, 1.95011, ‘Bi’)
.add_atom(4.1902, 0.00286053, 12.07, ‘Bi’)
.add_atom(16.7392, -12.0799, 1.95011, ‘Bi’)
.add_atom(18.8363, -10.8694, 12.07, ‘Bi’)
.add_atom(18.8324, -8.45583, 1.95011, ‘Bi’)
.add_atom(20.9296, -7.24533, 12.07, ‘Bi’)
.add_atom(4.18495, -4.83174, 1.95011, ‘Bi’)
.add_atom(6.28212, -3.62123, 12.07, ‘Bi’)
.add_atom(6.27823, -1.20764, 1.95011, ‘Bi’)
.add_atom(8.37539, 0.00286026, 12.07, ‘Bi’)
.add_atom(20.9244, -12.0799, 1.95011, ‘Bi’)
.add_atom(23.0215, -10.8694, 12.07, ‘Bi’)
.add_atom(6.27687, -8.45583, 1.95011, ‘Bi’)
.add_atom(8.37404, -7.24533, 12.07, ‘Bi’)
.add_atom(8.37014, -4.83174, 1.95011, ‘Bi’)
.add_atom(10.4673, -3.62123, 12.07, ‘Bi’)
.add_atom(10.4634, -1.20764, 1.95011, ‘Bi’)
.add_atom(12.5606, 0.00286041, 12.07, ‘Bi’)
.add_atom(8.36879, -12.0799, 1.95011, ‘Bi’)
.add_atom(10.466, -10.8694, 12.07, ‘Bi’)
.add_atom(10.4621, -8.45583, 1.95011, ‘Bi’)
.add_atom(12.5592, -7.24533, 12.07, ‘Bi’)
.add_atom(12.5553, -4.83174, 1.95011, ‘Bi’)
.add_atom(14.6525, -3.62123, 12.07, ‘Bi’)
.add_atom(14.6486, -1.20764, 1.95011, ‘Bi’)
.add_atom(16.7458, 0.00286038, 12.07, ‘Bi’)
.add_atom(12.557, -12.0782, 8.16974, ‘Bi’)
.add_atom(14.6542, -10.8677, 18.2896, ‘Bi’)
.add_atom(14.6503, -8.45414, 8.16974, ‘Bi’)
.add_atom(16.7474, -7.24363, 18.2896, ‘Bi’)
.add_atom(16.7435, -4.83004, 8.16974, ‘Bi’)
.add_atom(18.8407, -3.61954, 18.2896, ‘Bi’)
.add_atom(18.8368, -1.20595, 8.16974, ‘Bi’)
.add_atom(20.934, 0.00455848, 18.2896, ‘Bi’)
.add_atom(16.7422, -12.0782, 8.16974, ‘Bi’)
.add_atom(18.8393, -10.8677, 18.2896, ‘Bi’)
.add_atom(18.8355, -8.45414, 8.16974, ‘Bi’)
.add_atom(20.9326, -7.24363, 18.2896, ‘Bi’)
.add_atom(20.9287, -4.83004, 8.16974, ‘Bi’)
.add_atom(23.0259, -3.61954, 18.2896, ‘Bi’)
.add_atom(6.28124, -1.20595, 8.16974, ‘Bi’)
.add_atom(8.3784, 0.00455877, 18.2896, ‘Bi’)
.add_atom(20.9274, -12.0782, 8.16974, ‘Bi’)
.add_atom(23.0245, -10.8677, 18.2896, ‘Bi’)
.add_atom(23.0206, -8.45414, 8.16974, ‘Bi’)
.add_atom(25.1178, -7.24363, 18.2896, ‘Bi’)
.add_atom(8.37315, -4.83004, 8.16974, ‘Bi’)
.add_atom(10.4703, -3.61954, 18.2896, ‘Bi’)
.add_atom(10.4664, -1.20595, 8.16974, ‘Bi’)
.add_atom(12.5636, 0.0045585, 18.2896, ‘Bi’)
.add_atom(25.1126, -12.0782, 8.16974, ‘Bi’)
.add_atom(27.2097, -10.8677, 18.2896, ‘Bi’)
.add_atom(10.4651, -8.45414, 8.16974, ‘Bi’)
.add_atom(12.5622, -7.24363, 18.2896, ‘Bi’)
.add_atom(12.5583, -4.83004, 8.16974, ‘Bi’)
.add_atom(14.6555, -3.61954, 18.2896, ‘Bi’)
.add_atom(14.6516, -1.20595, 8.16974, ‘Bi’)
.add_atom(16.7488, 0.00455848, 18.2896, ‘Bi’)
.add_atom(12.5581, -9.66178, 10.1199, ‘Se’)
.add_atom(14.6553, -8.45127, 20.2397, ‘Se’)
.add_atom(14.6514, -6.03768, 10.1199, ‘Se’)
.add_atom(16.7485, -4.82718, 20.2397, ‘Se’)
.add_atom(16.7447, -2.41359, 10.1199, ‘Se’)
.add_atom(18.8418, -1.20309, 20.2397, ‘Se’)
.add_atom(18.8379, 1.2105, 10.1199, ‘Se’)
.add_atom(12.562, -12.0754, 20.2397, ‘Se’)
.add_atom(16.7433, -9.66178, 10.1199, ‘Se’)
.add_atom(18.8405, -8.45127, 20.2397, ‘Se’)
.add_atom(18.8366, -6.03768, 10.1199, ‘Se’)
.add_atom(20.9337, -4.82718, 20.2397, ‘Se’)
.add_atom(20.9298, -2.41359, 10.1199, ‘Se’)
.add_atom(6.28624, -1.20309, 20.2397, ‘Se’)
.add_atom(6.28235, 1.2105, 10.1199, ‘Se’)
.add_atom(16.7472, -12.0754, 20.2397, ‘Se’)
.add_atom(20.9285, -9.66178, 10.1199, ‘Se’)
.add_atom(23.0257, -8.45127, 20.2397, ‘Se’)
.add_atom(23.0218, -6.03768, 10.1199, ‘Se’)
.add_atom(8.37816, -4.82718, 20.2397, ‘Se’)
.add_atom(8.37427, -2.41359, 10.1199, ‘Se’)
.add_atom(10.4714, -1.20309, 20.2397, ‘Se’)
.add_atom(10.4675, 1.2105, 10.1199, ‘Se’)
.add_atom(20.9324, -12.0754, 20.2397, ‘Se’)
.add_atom(25.1137, -9.66178, 10.1199, ‘Se’)
.add_atom(10.4701, -8.45127, 20.2397, ‘Se’)
.add_atom(10.4662, -6.03768, 10.1199, ‘Se’)
.add_atom(12.5634, -4.82718, 20.2397, ‘Se’)
.add_atom(12.5595, -2.41359, 10.1199, ‘Se’)
.add_atom(14.6566, -1.20309, 20.2397, ‘Se’)
.add_atom(14.6527, 1.2105, 10.1199, ‘Se’)
.add_atom(25.1176, -12.0754, 20.2397, ‘Se’)
.add_atom(14.6509, -10.8695, 6.60167, ‘Se’)
.add_atom(16.7481, -9.65903, 16.7215, ‘Se’)
.add_atom(16.7442, -7.24544, 6.60167, ‘Se’)
.add_atom(18.8414, -6.03493, 16.7215, ‘Se’)
.add_atom(18.8375, -3.62134, 6.60166, ‘Se’)
.add_atom(20.9346, -2.41084, 16.7215, ‘Se’)
.add_atom(4.18999, 0.00275116, 6.60167, ‘Se’)
.add_atom(6.28715, 1.21326, 16.7215, ‘Se’)
.add_atom(18.8361, -10.8695, 6.60167, ‘Se’)
.add_atom(20.9333, -9.65903, 16.7215, ‘Se’)
.add_atom(20.9294, -7.24544, 6.60166, ‘Se’)
.add_atom(23.0266, -6.03493, 16.7215, ‘Se’)
.add_atom(6.28191, -3.62134, 6.60166, ‘Se’)
.add_atom(8.37907, -2.41

primitive should be a no-op if structure already primitive

To avoid surprises, it will still return a new structure.

Re-include enum from original pylada

Some tests from testsuite failing when run from travis-ci

Hi -- I'm trying to build a conda package for pylada with some CI to build the package, run the testsuite, update my anaconda channel with the build artifact for macOS and linux.

Some of the tests in the testsuite fail when run on travis-ci -- the testsuite work's fine when run on my machine locally -- but same set of tests fail on macOS and linux when run in CI. I think that possibly the failure might have something to do with openmp -- but not really sure ... Thought I could ask and see if someone already knows the issue and possibly a fix? These are the tests that fail:

Total Test time (real) = 335.44 sec
The following tests FAILED:
	  6 - pylada.crystal.map_sites (Failed)
	 61 - pifunctional (Failed)
	 62 - pylada.process.call (Failed)
	 63 - pylada.process.iterator (Failed)
	 64 - pylada.process.program (Failed)
	 65 - pylada.process.jobfolder (Failed)
	 82 - pylada.notebooks.notebooks (Failed)

I'm attaching the full raw log from one of the travis-ci job's -- the output of ctest -V is near the end of file...

Many thanks for any help!

Reinstate some sort of testing for pip

travis setup fails to pip install

Looks like travis changed from git to https:

1.54s$ pip install --user git+git://github.com/$TRAVIS_REPO_SLUG@$TRAVIS_COMMIT
Collecting git+git://github.com/pylada/pylada-light@2d621843ea83b65559ec3131288ca38279dc3b8a