[CP2K-user] [CP2K:21847] Mismatch between CP2K computed Force constant (a.u)and Gaussian computed force constant(mDyne/angstrom)

Naina Sethi sethinaina336 at gmail.com
Mon Sep 22 10:04:40 UTC 2025
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Dear Beliz,
I'm sorry for not getting back to you sooner. 
I followed these steps:
git clone --recursive https://github.com/cp2k/cp2k.git cp2k
cd cp2k
cd tools/toolchain/
./install_cp2k_toolchain.sh --mpi-mode=openmpi --enable-cuda=no 
--with-openmpi

 However I got the error, attaching the snapshot:
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<double>::dmatrix()':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.hpp:101: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<std::complex<double> >::dmatrix()':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.hpp:101: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<double>::dmatrix(double*, int, int, 
sirius::la::BLACS_grid const&, int, int)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:61: 
undefined reference to 
`spla::MatrixDistribution::create_blacs_block_cyclic(ompi_communicator_t*, 
char, int, int, int,
 int)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<double>::dmatrix(double*, int, int)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:100: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<double>::dmatrix(int, int, sirius::la::BLACS_grid 
const&, int, int, sirius::memory_t)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:37: 
undefined reference to 
`spla::MatrixDistribution::create_blacs_block_cyclic(ompi_communicator_t*, 
char, int, int, int,
 int)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<double>::dmatrix(int, int, sirius::memory_t)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:76: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<double>::dmatrix(int, int, sirius::memory_pool&, 
std::__cxx11::basic_string<char, std::char_traits<char>, std:
:allocator<char> > const&)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:88: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<double>::dmatrix(int, int, sirius::la::BLACS_grid 
const&, int, int, sirius::memory_pool&)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:122: 
undefined reference to 
`spla::MatrixDistribution::create_blacs_block_cyclic(ompi_communicator_t*, 
char, int, int, int
, int)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<std::complex<double> >::dmatrix(std::complex<double>*, 
int, int, sirius::la::BLACS_grid const&, int, int)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:61: 
undefined reference to 
`spla::MatrixDistribution::create_blacs_block_cyclic(ompi_communicator_t*, 
char, int, int, int,
 int)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<std::complex<double> >::dmatrix(std::complex<double>*, 
int, int)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:100: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<std::complex<double> >::dmatrix(int, int, 
sirius::la::BLACS_grid const&, int, int, sirius::memory_t)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:37: 
undefined reference to 
`spla::MatrixDistribution::create_blacs_block_cyclic(ompi_communicator_t*, 
char, int, int, int,
 int)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<std::complex<double> >::dmatrix(int, int, 
sirius::memory_t)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:76: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<std::complex<double> >::dmatrix(int, int, 
sirius::memory_pool&, std::__cxx11::basic_string<char, std::char_tra
its<char>, std::allocator<char> > const&)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:88: 
undefined reference to 
`spla::MatrixDistribution::create_mirror(ompi_communicator_t*)'
/usr/bin/ld: ../../src/libsirius_cxx.a(dmatrix.cpp.o): in function 
`sirius::la::dmatrix<std::complex<double> >::dmatrix(int, int, 
sirius::la::BLACS_grid const&, int, int, sirius::memory_pool&)':
/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/src/core/la/dmatrix.cpp:122: 
undefined reference to 
`spla::MatrixDistribution::create_blacs_block_cyclic(ompi_communicator_t*, 
char, int, int, int
, int)'
collect2: error: ld returned 1 exit status
/opt/cp2k-master/tools/toolchain/install/openmpi-5.0.8/bin/mpicxx -O2 -fPIC 
-fno-omit-frame-pointer -fopenmp -g -mtune=native -Wall -O3 -DNDEBUG 
CMakeFiles/atom.dir/atom.cpp.o -o atom  -Wl,-rpath,/o
pt/intel/oneapi/mkl/latest/lib/intel64::::::::::::::::::::::: 
../../src/libsirius_cxx.a 
/opt/cp2k-master/tools/toolchain/install/gsl-2.8/lib/libgsl.a 
/opt/cp2k-master/tools/toolchain/install/libxc-7
.0.0/lib/libxc.a 
/opt/cp2k-master/tools/toolchain/install/spglib-2.5.0/lib/libsymspg.a 
/opt/cp2k-master/tools/toolchain/install/hdf5-1.14.6/lib/libhdf5.so.310.5.1 
-ldl /opt/cp2k-master/tools/toolcha
in/install/COSMA-2.7.0/lib/libcosta.a 
/opt/cp2k-master/tools/toolchain/install/libvdwxc-0.4.0/lib/libvdwxc.a 
/opt/cp2k-master/tools/toolchain/install/SpFFT-1.1.1/lib/libspfft.a 
-Wl,--start-group /op
t/intel/oneapi/mkl/latest/lib/intel64/libmkl_intel_lp64.so 
/opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_sequential.so 
/opt/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.so -Wl,--end-group 
-lpth







*read /opt/cp2k-master/tools/toolchain/install/SpLA-1.6.1/lib/libspla.a 
/opt/cp2k-master/tools/toolchain/install/gsl-2.8/lib/libgsl.a 
/opt/cp2k-master/tools/toolchain/install/gsl-2.8/lib/libgslcblas.a 
/opt/cp2k-master/tools/toolchain/install/openblas-0.3.30/lib/libopenblas.so 
-lm -ldl 
/opt/cp2k-master/tools/toolchain/install/pugixml-1.15/lib/libpugixml.amake[2]: 
*** [apps/atoms/CMakeFiles/atom.dir/build.make:119: apps/atoms/atom] Error 
1make[2]: Leaving directory 
'/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/build'make[1]: *** 
[CMakeFiles/Makefile2:314: apps/atoms/CMakeFiles/atom.dir/all] Error 
2make[1]: Leaving directory 
'/opt/cp2k-master/tools/toolchain/build/SIRIUS-7.7.0/build'make: *** 
[Makefile:139: all] Error 
2/opt/cp2k-master/tools/toolchain/scripts/tool_kit.sh: line 680: 
/opt/cp2k-master/tools/toolchain/install/sirius-7.7.0/install_successful: 
No such file or directory*
On Tuesday, September 16, 2025 at 5:24:58 PM UTC+5:30 Beliz Gökmen wrote:

> Hi Naina,
>
> Could you please share the exact steps you took for compiling CP2K 
> including the configuration you used?
>
> Best,
> Beliz
>
> On 16 Sep 2025, at 09:01, Naina Sethi <sethin... at gmail.com> wrote:
>
> Hi Dr. Beliz,
> I tried installing the developer version of CP2K; however, I couldn't 
> succeed.I was unable to complete the installation due to an issue with 
> the source code of *Sirius*, which is a required dependency for CP2K.
>
> Could you please suggest some solution?
>
> On Wednesday, September 10, 2025 at 7:34:40 PM UTC+5:30 Beliz Gökmen wrote:
>
>> Hi Naina,
>> Thanks for reporting this. You can find the updated code in the 
>> development version of cp2k <https://github.com/cp2k/cp2k>.
>> Best,
>> Beliz
>>
>> On Monday, 8 September 2025 at 05:17:23 UTC-5 Naina Sethi wrote:
>>
>>> Even with periodic none in subsystem gives same results.
>>>
>>> On Monday, September 8, 2025 at 2:43:25 PM UTC+5:30 Johann Pototschnig 
>>> wrote:
>>>
>>>> You are still missing the "PERIODIC NONE" in the SUBSYS section:
>>>>
>>>> https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.CELL.PERIODIC
>>>>
>>>> There is a warning in your output.
>>>>
>>>> On Friday, September 5, 2025 at 8:42:47 PM UTC+2 Naina Sethi wrote:
>>>>
>>>>> Dear Prof. Hutter,
>>>>> Is there any mistake in my input setup? Could you please help.
>>>>>
>>>>> On Monday, August 25, 2025 at 3:05:15 PM UTC+5:30 Naina Sethi wrote:
>>>>>
>>>>>> I am using CP2K version 2024.3 and attempted to reproduce one of the 
>>>>>> sample calculations on the benzene molecule (
>>>>>> https://www.cp2k.org/exercises:2015_ethz_mmm:infra_red). However, I 
>>>>>> am unable to obtain force constants similar to those that i get from 
>>>>>> gaussian. While the vibrational frequencies, IR intensities, and reduced 
>>>>>> masses agree perfectly with Gaussian results, the force constants differ 
>>>>>> significantly(specifically for lower frequency regime). This discrepancy is 
>>>>>> concerning because the magnitude of the force constants is critical for my 
>>>>>> work. Could you please advise whether this might be related to changes in 
>>>>>> the code since the example was prepared, or if I might be missing something 
>>>>>> in my setup?
>>>>>>
>>>>>> I am attaching the Input and output files from CP2K and gaussian 
>>>>>> calculation. Kindly suggest. 
>>>>>>
>>>>>> Thank you very much for your time and guidance.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>>
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# 1. Update & install prerequisites

sudo dnf groupinstall "Development Tools" -y
sudo dnf install -y wget git \
     gcc gcc-c++ gcc-gfortran \
     openmpi openmpi-devel \
     blas blas-devel lapack lapack-devel \
     fftw fftw-devel \
     libtool \
     python3 python3-devel \
     zlib-devel

# 2. Clone CP2K

cd ~/build
git clone --recursive (https://github.com/cp2k/cp2k.git cp2k) --- Paste Your Link hear.
 or 
Download from Web

cd cp2k

# 3. Run toolchain

cd tools/toolchain
./install_cp2k_toolchain.sh --with-openmpi \
    --with-openblas=system \
    --with-fftw=system \
    --with-libxc=yes \
    --with-libint=yes

 or 

/install_cp2k_toolchain.sh --mpi-mode=openmpi --enable-cuda=no --with-openmpi
 

# 4. Set up ARCH file

cd ../..   # back to cp2k root
# Use an existing arch file or adapt one
ARCHFILE=arch/Linux-gnu-x86_64.psmp
# Optionally edit it:
# sed -i 's|MPI_COMPILER=.*|MPI_COMPILER=mpif90|g' $ARCHFILE
# sed -i 's|FC_FLAGS=.*|FC_FLAGS="${FC_FLAGS} -O3 -march=native"|g' $ARCHFILE

# 5. Compile

make -j $(nproc) ARCH=Linux-gnu-x86_64 VERSION=psmp

# 6. (Optional) test

make ARCH=Linux-gnu-x86_64 VERSION=psmp test

# 7. Install / set up PATH (example)

mkdir -p ~/local/bin
cp exe/Linux-gnu-x86_64/psmp/cp2k.popt ~/local/bin/cp2k     # or cp2k.psmp etc.

echo 'export PATH=~/local/bin:$PATH' >> ~/.bashrc
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