[CP2K-user] [CP2K:21848] Mismatch between CP2K computed Force constant (a.u)and Gaussian computed force constant(mDyne/angstrom)

Johann Pototschnig pototschnig.johann at gmail.com
Mon Sep 22 11:07:17 UTC 2025
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Hello Naina,

You should be ale to deactivate Sirius via: 
--with-sirius=no
 if you don't need the plane wave computations. 

 The error indicates that SPLA is missing/defective. Do you have an error 
message for this? 

The options for the --with-...= are 
=no
=install
=${PATH}
I don't think "yes" works. 

I think you you should use the tools/toolchain/install/arch/local.psmp
which is generated by the toolchain script for your setup. 

The toolchain is no longer the preferred method of installation. you could 
try a different installation option. 

best wishes,
Johann

On Monday, September 22, 2025 at 12:04:41 PM UTC+2 Naina Sethi wrote:

> 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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>>
>>
>>

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