quantum-dynamics-hub / libra-code Goto Github PK

Home Page: https://quantum-dynamics-hub.github.io/libra/index.html

License: GNU General Public License v3.0

CMake 0.32% Python 16.30% Gnuplot 1.02% Shell 0.08% C++ 21.53% Roff 35.75% Tcl 0.01% Jupyter Notebook 24.87% D 0.12%

nonadiabatic quantum quantum-chemistry dynamics molecular-dynamics do-it-yourself library methodology-development electronic-structure semiempirical-methods

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minor mistake about some comments

I found a minor mistake about the comments on https://github.com/Quantum-Dynamics-Hub/libra-code/blob/55dd61b998f070bdcb7b7fcc994bc1289d09dc1a/src/math_meigen/mEigen_eigensolve.cpp . Here, H * C = (N_bas x N_bas) x ( N_bas x N_mo ) = N_mo x N_mo
seems to be
H * C = (N_bas x N_bas) x ( N_bas x N_mo ) = N_bas x N_mo.

Latest version depends on an unreleased version of Libint ?

Building Libra fails on my system with:

CMake Error at CMakeLists.txt:94 (FIND_PACKAGE):
  Could not find a package configuration file provided by "Libint2"
  (requested version 2.7.0) with any of the following names:

    Libint2Config.cmake
    libint2-config.cmake

  Add the installation prefix of "Libint2" to CMAKE_PREFIX_PATH or set
  "Libint2_DIR" to a directory containing one of the above files.  If
  "Libint2" provides a separate development package or SDK, be sure it has
  been installed.

Latest release version of Libint is 2.6.0 (https://github.com/evaleev/libint/releases/tag/v2.6.0) What's going on ?

a couple of questions on the parameter settings in the step4 of the Libra/CP2K workflow for NA-MD

I am doing some testing calculations using the Libra/CP2K workflow for NA-MD. I have a couple of questions on the parameter settings in step4_cp2k.

What is params['istate'] used for? In the README.md file, it is explained that both init_states and params['istate'] contain the initial states to start the dynamics from. What is the difference between these two parameters?
In the params_common, the initial nuclear configurations are determined by "x0":[-4.0], "p0":[4.0], "masses":[2000.0], "k":[0.01] , How to choose the proper values for these parameters for specific systems?
Along with Q2, is it possible to use the nuclear configurations from the MD trajectory in step1 as the initial conditions for the nuclear part, which was adopted in the Libra/QE NA-MD workflow?
Thanks a lot for your help.

New GFSH function can't be called correctly.

I modified the script
(see https://github.com/kosukesato/libra-code/blob/devel/developments/fragments-namd/run_aa_md-eht_2c.py );
here, new GFSH function you exported recently can be called. Then, I called the function and found an error message saying
*** glibc detected *** python: double free or corruption (out): 0x00007fffa54958a0 ***.
Such a message wasn't seen with MSSH or FSSH scheme. If you know why this occurs, could you fix this problem?

thank you.

AttributeError: module 'libra_py' has no attribute 'Gaussian_methods'

Hi,
I have successfully compiled libra-code (v5.5.0) with anaconda in following steps:

conda remove --name libra --all  
conda create -n libra python=3.7
conda activate libra
conda install -y -c conda-forge numpy scipy matplotlib imageio jupyter_core
conda install -y ipykernel
conda install -y -c rmg py3dmol
#Next, all what we actually need:
conda install -y conda-build make
conda install -y -c conda-forge gcc_linux-64=12.2.0 gxx_linux-64=12.2.0 cmake=3.24.2 boost=1.80.0 python-devtools llvm-openmp
conda install -y -c conda-forge/label/gcc7 eigen mpfr
conda install -y -c psi4/label/dev libint2=2.7.1
conda install -y -c anaconda h5py gmp
cd ~/app/
git clone https://github.com/Quantum-Dynamics-Hub/libra-code.git libra
cd libra
git checkout devel
mkdir _build && cd _build && cmake ../
make -j4  
export PYTHONPATH=/home/mpiusr/app/libra/_build/src:$PYTHONPATH

But, I encountered some issues when I run the test jobs in libra-code, the following errors appear:

(libra) [mpiusr@ws1 test_1_init_system]$ python run_test.py 

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > already registered; second conversion method ignored.

  return f(*args, **kwds)

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >, false> > already registered; second conversion method ignored.

  return f(*args, **kwds)

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > > already registered; second conversion method ignored.

  return f(*args, **kwds)

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > >, false> > already registered; second conversion method ignored.

  return f(*args, **kwds)

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > already registered; second conversion method ignored.

  return f(*args, **kwds)

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, false> > already registered; second conversion method ignored.

  return f(*args, **kwds)

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for std::vector<std::vector<std::complex<double>, std::allocator<std::complex<double> > >, std::allocator<std::vector<std::complex<double>, std::allocator<std::complex<double> > > > > already registered; second conversion method ignored.

  return f(*args, **kwds)

/home/mpiusr/app/anaconda/3/envs/libra/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: to-Python converter for boost::python::detail::container_element<std::vector<std::vector<std::complex<double>, std::allocator<std::complex<double> > >, std::allocator<std::vector<std::complex<double>, std::allocator<std::complex<double> > > > >, unsigned long, boost::python::detail::final_vector_derived_policies<std::vector<std::vector<std::complex<double>, std::allocator<std::complex<double> > >, std::allocator<std::vector<std::complex<double>, std::allocator<std::complex<double> > > > >, false> > already registered; second conversion method ignored.

  return f(*args, **kwds)

Traceback (most recent call last):

  File "run_test.py", line 23, in <module>

    from libra_py import *

AttributeError: module 'libra_py' has no attribute 'Gaussian_methods'

I would greatly appreciate your assistance in resolving these issues.

possible bug in hpc.utils.py

From Fulu Zheng:

Hi Alexey, I think there might be a minor problem in the “distribute” function in the hpc.utils.py. In lines 166 and 167:

   Nstart = 0
   Nend = max_steps-1

I think the correct values for Nstart and Nend should be

  Nstart = Nmin
  Nend = Nmin + max_steps-1

Otherwise, it will not not work if we start from nonzero steps.

libra_py.tsh is deprecated but still imported in step3.py

Hello, apologies if I'm doing anything wrong here.

But I've noticed that on brand new installations of Libra, when attempting to run a python script that calls functions within the libra_py.workflows.nbra.step3 file, that step3.py file has an import here which attempts to import a libra_py.tsh file. This file does not exist in this location. If I look inside libra_py folder I can see there is a tsh_stat.py file but no tsh.py file.

Having searched the repository for the function that step3.py wants to call from tsh.py file, I find that a tsh.py file does actually exist within the repository and contain the code that looks right to me but this tsh.py file exists inside a folder called "deprecated_code/python". Copying this file verbatim in to the location that step3.py expects it to exist in fixes this import error.

To be more specific, the exact command run inside the libra root directory is
cp deprecated_code/python/tsh.py _build/src/libra_py/

I haven't been able to track down whether these functions are actually being called. Should the tsh.py file really be deprecated? Or should the functions that utilize it also be deprecated? Either way, step3 and any other files which expect tsh.py in libra_py will not function currently.

The MD tutorial files in tests/test_md are not updated

The details are attached in a pdf file : Libra Molecular Dynamics Error.pdf

ida_py

ida_py function has a problem about initializing time coefficients c=q+ip of electronic objects.
Would you fix it?

Actual installation instructions ?

Is there a way to actually install this software ?
Building and then editing .bashrc files and setting path is hardly an installation.
https://quantum-dynamics-hub.github.io/libra/installation.html

How about a "make install" target ? or a way to build a python wheel that can then be installed with pip ?

I tried

[mboisson@build-node build]$ make install
make: *** No rule to make target 'install'.  Stop

I tried

[mboisson@build-node libra-code-5.0.0]$ python setup.py bdist_wheel
running bdist_wheel
running build
running build_py
running egg_info
writing Libra.egg-info/PKG-INFO
writing dependency_links to Libra.egg-info/dependency_links.txt
writing top-level names to Libra.egg-info/top_level.txt
reading manifest file 'Libra.egg-info/SOURCES.txt'
writing manifest file 'Libra.egg-info/SOURCES.txt'
UPDATING build/lib/src/_version.py
error: [Errno 2] No such file or directory: 'build/lib/src/_version.py'

Memory leak

void DIIS::update_diis_coefficients function in file src/solvers/DIIS.cpp, MatrixXd* A may have memory leaks.

Use cmake-build-extention

This is just a suggestion, but as someone who just finished building you project for one of our user's on the Canadian super computer systems where conda is entirely broken and setting LD_LIBRARY_PATH causes a lot of pain, I think your project could really benefit from using the setuptools cmake-build-extension.

Ideally then an install could then become as easy as

pip install .

inside a virtual environment, and there would be no need to mess around with PATH, LD_LIBRARY_PATH, or PYTHON_PATH to use to package as well.

make libint2 errors

Getting compile error, even after trying to use solutions from previous issue.
make[2]: *** [src/libint2_wrappers/CMakeFiles/libint2_wrappers.dir/build.make:95: src/libint2_wrappers/CMakeFiles/libint2_wrappers.dir/liblibint2_wrappers.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:2612: src/libint2_wrappers/CMakeFiles/libint2_wrappers.dir/all] Error 2 [ 51%] Linking CXX shared library libmolint.so [ 51%] Built target molint [ 51%] Linking CXX shared library libqobjects.so [ 51%] Built target qobjects make: *** [Makefile:103: all] Error 2
I have libint2 2.6.0 and as recommended here (#121) changed CMakeLists.txt, nothing helped.

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