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sp2's Introduction

sp2

Computational physics research application dealing mainly with carbon-based structures (e.g. graphene, carbon nanotubes) developed at the ICMP research group by Colin Daniels and Michael Lamparski. A web interface to some of the Raman functionality is available here.

Disclaimer: sp2 is very much research code, and has hardly followed best practices in terms of development. As such, some features may not work and it is unfortunately very possible that the exact code used for a particular publication may not even be present in the git commit history. The code itself is reproduced here for reference, and in particular the Raman functionality has been superceded by rsp2.

Installation

There are only a few dependencies, the primary ones being MPI, boost, python 3, and phonopy. Look at the GitHub workflow file if totally lost, since it does build fine in that environment.

Related Publications

Below is a list of publications in which this software was utilized at least in part.

  • J. Overbeck, G. B. Barin, C. Daniels, M. L. Perrin, O. Braun, Q. Sun, R. Darawish, M. De Luca, X.-Y. Wang, T. Dumslaff, A. Narita, K. Müllen, P. Ruffieux, V. Meunier, R. Fasel, and M. Calame, A Universal Length-Dependent Vibrational Mode in Graphene Nanoribbons, ACS Nano 10.1021/acsnano.9b05817 (2019).
  • O. Gröning, S. Wang, X. Yao, C. A. Pignedoli, G. B. Barin, C. Daniels, A. Cupo, V. Meunier, X. Feng, A. Narita, K. Müllen, P. Ruffieux, and R. Fasel, Engineering of Robust Topological Quantum Phases in Graphene Nanoribbons, Nature 560, 209 10.1038/s41586-018-0375-9 (2018).
  • J. R. Owens, C. Daniels, A. Nicolaï, H. Terrones, and V. Meunier, Structural, Energetic, and Electronic Properties of Gyroidal Graphene Nanostructures, Carbon 96, 998 10.1016/j.carbon.2015.10.042 (2016).
  • Z. J. Qi, C. Daniels, S. J. Hong, Y. W. Park, V. Meunier, M. Drndić, and A. T. C. Johnson, Electronic Transport of Recrystallized Freestanding Graphene Nanoribbons, ACS Nano 9, 3510 10.1021/nn507452g (2015).
  • A. Nicolaï, J. Monti, C. Daniels, and V. Meunier, Electrolyte Diffusion in Gyroidal Nanoporous Carbon, J. Phys. Chem. C 119, 2896 10.1021/jp511919d (2015).
  • C. Daniels, A. Horning, A. Phillips, D. V. P. Massote, L. Liang, Z. Bullard, B. G. Sumpter, and V. Meunier, Elastic, Plastic, and Fracture Mechanisms in Graphene Materials, J. Phys.: Condens. Matter 27, 373002 10.1088/0953-8984/27/37/373002 (2015).
  • C. Daniels, Z. Bullard, E. C. Girão, and V. Meunier, Emergent Magnetism in Irradiated Graphene Nanostructures, Carbon 78, 196 10.1016/j.carbon.2014.06.072 (2014).

References

sp2 would not be possible without building upon the following works:

  • A. N. Kolmogorov and V. H. Crespi, Registry-Dependent Interlayer Potential for Graphitic Systems, Phys. Rev. B 71, 235415 10.1103/PhysRevB.71.235415 (2005).
  • A. Togo and I. Tanaka, First Principles Phonon Calculations in Materials Science, Scripta Materialia 108, 1 10.1016/j.scriptamat.2015.07.021 (2015).
  • D. W. Brenner, O. A. Shenderova, J. A. Harrison, S. J. Stuart, B. Ni, and S. B. Sinnott, A Second-Generation Reactive Empirical Bond Order (REBO) Potential Energy Expression for Hydrocarbons, J. Phys.: Condens. Matter 14, 783 10.1088/0953-8984/14/4/312 (2002).
  • E. Bitzek, P. Koskinen, F. Gähler, M. Moseler, and P. Gumbsch, Structural Relaxation Made Simple, Phys. Rev. Lett. 97, 170201 10.1103/PhysRevLett.97.170201 (2006).
  • N. Andrei, Conjugate gradient algorithms for molecular formation under pairwise potential minimization, in Mathematical Modeling of Environmental and Life Sciences Problems camo.ici.ro/neculai/potential.pdf (Constanta, Romania, 2008).
  • R. Saito, M. Furukawa, G. Dresselhaus, and M. S. Dresselhaus, Raman Spectra of Graphene Ribbons, J. Phys.: Condens. Matter 22, 334203 10.1088/0953-8984/22/33/334203 (2010).
  • S. Guha, J. Menéndez, J. B. Page, and G. B. Adams, Empirical Bond Polarizability Model for Fullerenes, Phys. Rev. B 53, 13106 10.1103/PhysRevB.53.13106 (1996).
  • S. J. Stuart, A. B. Tutein, and J. A. Harrison, A Reactive Potential for Hydrocarbons with Intermolecular Interactions, The Journal of Chemical Physics 112, 6472 10.1063/1.481208 (2000).
  • S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, Journal of Computational Physics 117, 1 10.1006/jcph.1995.1039 (1995).
  • Z. Bullard and V. Meunier, Dynamical Properties of Carbon Nanotube Welding into X Junctions, Phys. Rev. B 88, 035422 10.1103/PhysRevB.88.035422 (2013).
  • Z.-H. Zhan, J. Zhang, Y. Li, and H. S.-H. Chung, Adaptive Particle Swarm Optimization, IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics) 39, 1362 10.1109/TSMCB.2009.2015956 (2009).

sp2's People

Contributors

colin-daniels avatar exphp avatar

Watchers

avatar avatar avatar

sp2's Issues

truly, honestly to god doing zero iterations in acgsd

doing zero iterations with #12:

Using steepest descent.
 i:      0  v:   -11852.025739365 dv: -1.042281e-09  g:  6.937322e-05 
ACGSD Finished.

as evidenced by the presence of a "dv" value, even zero iterations does at least one full iteration and I believe it can potentially change the position.

I don't actually see any way to fix this that isn't horribly disgusting, because the control flow logic in the function is already so complicated. If I had two days worth of time to throw at it, I'd probably try to refactor out all the control flow logic into some sort of state machine first

consider scaling grad_norm by N

note: the problem colin mentioned with doing this is that acgsd isn't supposed to know about the meaning or shape of the position vector (although it does already have grad_max which assumes that all elements are "alike" in meaning)

polarization_axes serialization

sp2 currently relies on the non-error-throwing behavior of deserialize_basic to handle polarization_axes. If I understand correctly, this option accepts multiple types? (either an array or the string "backscatter_avg")

I tried getting it in there proper, but clearly I've been away from C++ for too long, as I can only regard the current compiler error I'm getting as complete nonsense (if "io is not declared", then how on earth is the rest of that file okay?), so I'm shelving it for now

my broken/untested/probably unidiomatic edit: https://github.com/ExpHP/sp2/commit/e6d300056e511a0078bd0223276ef81746d6822e

Trouble building in ubuntu 20.04

Commands run

sudo apt install cmake libopenmpi-dev libboost-all-dev libfreetype-dev

git clone https://github.com/colin-daniels/sp2
cd sp2

python3 -m venv venv
. ./venv/bin/activate
python3 -m pip install wheel
python3 -m pip install -r <(grep numpy requirements.txt)
python3 -m pip install -r requirements.txt

mkdir build
cd build

cmake .. -DCMAKE_BUILD_TYPE=Release

Versions

   $ cmake --version
cmake version 3.16.3
   $ mpic++ --version
g++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
   $ grep 'e BOOST_LIB_VERSION' /usr/include/boost/version.hpp
#define BOOST_LIB_VERSION "1_71"
   $ python3 --version
Python 3.8.10

What happens

cmake generates a large number of warnings that look like this:

CMake Warning (dev) at deps/boost-mpi/CMakeLists.txt:24 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

until finally the following occurs:

-- Performing Test SP2_CAN_HASH_ENUM
-- Performing Test SP2_CAN_HASH_ENUM - Success
-- VERSION: sp2_VERSION
-- VERSION: 0.1
-- Configuring done
CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::mpi" but the target was not found.
  Perhaps a find_package() call is missing for an IMPORTED target, or an
  ALIAS target is missing?


CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::serialization" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::mpi" but the target was not found.
  Perhaps a find_package() call is missing for an IMPORTED target, or an
  ALIAS target is missing?


CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::serialization" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


-- Generating done
CMake Generate step failed.  Build files cannot be regenerated correctly.

Full CMake output

Full cmake output 
-- The CXX compiler identification is GNU 9.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.71.0/BoostConfig.cmake (found version "1.71.0") found components: mpi serialization
CMake Warning (dev) at deps/boost-mpi/CMakeLists.txt:24 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at deps/boost-mpi/CMakeLists.txt:24 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at deps/boost-mpi/CMakeLists.txt:24 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    Boost::mpi

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at deps/boost-mpi/CMakeLists.txt:24 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    Boost::serialization

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

Cloning into 'cxxopts-src'...
Note: switching to 'v2.2.0'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at e6858d3 Add to changelog for #170
-- cxxopts version 2.2.0
-- The C compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
CMake Warning (dev) at deps/cxxopts/CMakeLists.txt:12 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    cxxopts

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

Cloning into 'jsoncpp-src'...
Note: switching to '1.8.3'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 2de1802 Merge pull request #655 from cdunn2001/fix-649
-- JsonCpp Version: 1.8.3
-- Looking for C++ include clocale
-- Looking for C++ include clocale - found
-- Looking for localeconv
-- Looking for localeconv - found
-- Looking for C++ include sys/types.h
-- Looking for C++ include sys/types.h - found
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
-- Looking for C++ include stddef.h
-- Looking for C++ include stddef.h - found
-- Check size of lconv
-- Check size of lconv - done
-- Performing Test HAVE_DECIMAL_POINT
-- Performing Test HAVE_DECIMAL_POINT - Success
CMake Warning (dev) at deps/jsoncpp/CMakeLists.txt:16 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    jsoncpp_lib_static

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
CMake Warning (dev) at deps/lammps/CMakeLists.txt:81 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    lammps

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonInterp: /home/exp/asd/clone/thpages/sp2/venv/bin/python3 (found suitable version "3.8.10", minimum required is "3")
-- Found PYMOD_PHONOPY: /home/exp/asd/clone/thpages/sp2/venv/lib/python3.8/site-packages/phonopy
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so (found suitable version "3.8.10", minimum required is "3")
-- Found NumPy: /home/exp/asd/clone/thpages/sp2/venv/lib/python3.8/site-packages/numpy/core/include (found version "1.16.4")
CMake Warning (dev) at deps/python/CMakeLists.txt:8 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    /usr/lib/x86_64-linux-gnu/libpython3.8.so

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at deps/randutils/CMakeLists.txt:9 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    randutils

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

Cloning into 'templ-src'...
Note: switching to '5c2dd1d36b107cbeb5fc46a99b5775bbee355cad'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 5c2dd1d Standardized some names in basic.hpp, added is_reference_wrapper and ic.
-- Performing Test TEMPL_CAN_DEDUCT_SELECT
-- Performing Test TEMPL_CAN_DEDUCT_SELECT - Success
CMake Warning (dev) at deps/templ/CMakeLists.txt:11 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    templ

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

Cloning into 'yaml-cpp-src'...
Note: switching to 'yaml-cpp-0.6.3'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 9a36242 Update version to 0.6.3.
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
CMake Warning (dev) at deps/yaml-cpp/CMakeLists.txt:15 (target_link_libraries):
  Policy CMP0079 is not set: target_link_libraries allows use with targets in
  other directories.  Run "cmake --help-policy CMP0079" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target

    project-deps

  is not created in this directory.  For compatibility with older versions of
  CMake, link library

    yaml-cpp

  will be looked up in the directory in which the target was created rather
  than in this calling directory.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Performing Test SP2_CAN_HASH_ENUM
-- Performing Test SP2_CAN_HASH_ENUM - Success
-- VERSION: sp2_VERSION
-- VERSION: 0.1
-- Configuring done
CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::mpi" but the target was not found.
  Perhaps a find_package() call is missing for an IMPORTED target, or an
  ALIAS target is missing?


CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::serialization" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::mpi" but the target was not found.
  Perhaps a find_package() call is missing for an IMPORTED target, or an
  ALIAS target is missing?


CMake Error at src/CMakeLists.txt:192 (add_executable):
  Target "sp2" links to target "Boost::serialization" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


-- Generating done
CMake Generate step failed.  Build files cannot be regenerated correctly.

Further details

I'm not sure that the warnings are actually related to the final error; I tried adding

cmake_policy(SET CMP0079 OLD)

to the CMakeLists.txt and this eliminates most of the warnings, but not the Boost errors that prevent compilation.

cannot use cmake (multiple targets named "gmock")

The repo is not buildable; it looks like the cmake config tries to add the same dependency multiple times

[ lampam @ 10:35:04 ] (master) ~/asd/clone/sp2/build
$ cmake ..
-- The CXX compiler identification is GNU 5.4.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Cloning into 'googletest-src'...
Already on 'master'
-- The C compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found PythonInterp: /usr/bin/python (found version "2.7.12") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
Cloning into 'templ-src'...
Already on 'master'
Cloning into 'jsoncpp-src'...
Already on 'master'
-- JsonCpp Version: 1.8.0
-- Looking for C++ include clocale
-- Looking for C++ include clocale - found
-- Looking for localeconv
-- Looking for localeconv - found
-- Looking for C++ include sys/types.h
-- Looking for C++ include sys/types.h - found
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
-- Looking for C++ include stddef.h
-- Looking for C++ include stddef.h - found
-- Check size of lconv
-- Check size of lconv - done
-- Performing Test HAVE_DECIMAL_POINT
-- Performing Test HAVE_DECIMAL_POINT - Success
-- Found PythonInterp: /usr/bin/python (found suitable version "2.7.12", minimum required is "2.6") 
Cloning into 'yaml-cpp-src'...
Already on 'master'
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
-- Found PythonInterp: /usr/bin/python (found version "2.7.12") 
CMake Error at build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:130 (add_library):
  add_library cannot create target "gtest" because another target with the
  same name already exists.  The existing target is a static library created
  in source directory
  "/home/lampam/asd/clone/sp2/build/googletest-src/googletest".  See
  documentation for policy CMP0002 for more details.
Call Stack (most recent call first):
  build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:153 (cxx_library_with_type)
  build/yaml-cpp-src/test/gmock-1.7.0/gtest/CMakeLists.txt:70 (cxx_library)


CMake Error at build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:130 (add_library):
  add_library cannot create target "gtest_main" because another target with
  the same name already exists.  The existing target is a static library
  created in source directory
  "/home/lampam/asd/clone/sp2/build/googletest-src/googletest".  See
  documentation for policy CMP0002 for more details.
Call Stack (most recent call first):
  build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:153 (cxx_library_with_type)
  build/yaml-cpp-src/test/gmock-1.7.0/gtest/CMakeLists.txt:71 (cxx_library)


CMake Error at build/yaml-cpp-src/test/gmock-1.7.0/gtest/CMakeLists.txt:72 (target_link_libraries):
  Attempt to add link library "gtest" to target "gtest_main" which is not
  built in this directory.


CMake Error at build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:130 (add_library):
  add_library cannot create target "gmock" because another target with the
  same name already exists.  The existing target is a static library created
  in source directory
  "/home/lampam/asd/clone/sp2/build/googletest-src/googlemock".  See
  documentation for policy CMP0002 for more details.
Call Stack (most recent call first):
  build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:153 (cxx_library_with_type)
  build/yaml-cpp-src/test/gmock-1.7.0/CMakeLists.txt:74 (cxx_library)


CMake Error at build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:130 (add_library):
  add_library cannot create target "gmock_main" because another target with
  the same name already exists.  The existing target is a static library
  created in source directory
  "/home/lampam/asd/clone/sp2/build/googletest-src/googlemock".  See
  documentation for policy CMP0002 for more details.
Call Stack (most recent call first):
  build/yaml-cpp-src/test/gmock-1.7.0/gtest/cmake/internal_utils.cmake:153 (cxx_library_with_type)
  build/yaml-cpp-src/test/gmock-1.7.0/CMakeLists.txt:79 (cxx_library)


-- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so  
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   mpi
--   serialization
-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.5.2", minimum required is "3") 
-- Found PYMOD_PHONOPY: /usr/local/lib/python3.5/dist-packages/phonopy  
-- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.12", minimum required is "2.7") 
-- Configuring incomplete, errors occurred!

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