quantum-dynamics-hub / libra-code Goto Github PK
View Code? Open in Web Editor NEWHome Page: https://quantum-dynamics-hub.github.io/libra/index.html
License: GNU General Public License v3.0
Home Page: https://quantum-dynamics-hub.github.io/libra/index.html
License: GNU General Public License v3.0
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
.
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 ?
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.
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?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?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.
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.
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.
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 details are attached in a pdf file : Libra Molecular Dynamics Error.pdf
ida_py function has a problem about initializing time coefficients c=q+ip of electronic objects.
Would you fix it?
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'
void DIIS::update_diis_coefficients function in file src/solvers/DIIS.cpp, MatrixXd* A may have memory leaks.
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.
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.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.