Hello everyone,
I am new to using LAMMPS and OpenKIM. I am trying to use “Dipole_Umeno_YSZ__MO_394669891912_001”. I followed all the steps mentioned in the installation guide and I am able to run other models except the one mentioned above. I am currently working with “lammps-23-June-2022” and “kim_api 2.2.1”. When trying to add this model, I get an error message:
(base) tejesh@tejesh-VirtualBox:~/Documents/lammps-23Jun2022/lib/kim/installed-2.2.1/bin$ kim-api-collections-management install system Dipole_Umeno_YSZ__MO_394669891912_001
*** ERROR *** Dipole_Umeno_YSZ__MO_394669891912_001 found at openkim.org is not compatible with this version of the KIM API.
So, I tried working with an older version of lammps and OpenKIM. I tried using “lammps-22Aug-2018” and “kim_api 1.9.5” and got the following error message:
(base) tejesh@tejesh-VirtualBox:~/Documents/lammps-22Aug18/lib/kim/installed-kim-api-v1.9.5/bin$ kim-api-collections-management install system Dipole_Umeno_YSZ__MO_394669891912_001
*** ERROR *** Dipole_Umeno_YSZ__MO_394669891912_001 found at openkim.org requires version 1.6 of the KIM API which is not compatible with the installed version 2 of the KIM API.
So I am now trying to use “kim_api 1.6.0” with “lammps-22Aug-2018” and got the following error:
(base) tejesh@tejesh-VirtualBox:~/Downloads/lammps-22Aug18/lib/kim/kim-api-v1.6.0$ make add-Dipole_Umeno_YSZ__MO_394669891912_001
adding… Dipole_Umeno_YSZ__MO_394669891912_001 … to /home/tejesh/Downloads/lammps-22Aug18/lib/kim/kim-api-v1.6.0/src/models
Unable to download Dipole_Umeno_YSZ__MO_394669891912_001 from https://openkim.org. Check the KIM Item ID for errors.
Makefile:185: recipe for target ‘add-Dipole_Umeno_YSZ__MO_394669891912_001’ failed
make: *** [add-Dipole_Umeno_YSZ__MO_394669891912_001] Error 1
I would really appreciate if someone could help me this.
Thank you for your time!
Thanks for your message. It looks like openkim.org used to have tgz files in addition to txz files, but now there are only txz files. The kim-api-v1.6.0 is looking for the tgz file and can’t find it.
We’re working on a 2.0 version of the Umeno model, but it may take some time for us to finalize it. So, in the meantime the best I can suggest is for you to use a more “manual” process to get this model.
To do this you’ll want to download the Umeno *.tgz file and unpack it into the kim-api-v1.6.0/src/models/ subdirectory. I believe that once you do this, and then build and install the kim-api the model will also be built and installed. Hope that works for you. Let us know if you run into further problems.
Thank you for your response, Ryan. I was able to add the Umeno model successfully and build kim-api. However, when I tried building lammps, I got the following error:
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_temp_deform.cpp
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/respa.cpp
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/dump_custom.cpp
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_pe.cpp
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/fix_vector.cpp
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/molecule.cpp
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/fix_temp_csvr.cpp
make[1]: kim-api-build-config: Command not found
mpicxx -g -O3 -DLAMMPS_GZIP -I…/…/lib/meam -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/pair_kim.cpp
…/pair_kim.cpp:42:10: fatal error: KIM_API.h: No such file or directory #include “KIM_API.h”
^~~~~~~~~~~
compilation terminated.
Makefile:102: recipe for target ‘pair_kim.o’ failed
make[1]: *** [pair_kim.o] Error 1
make[1]: Leaving directory ‘/home/tejesh/Downloads/lammps-10Feb15/src/Obj_mpi’
Makefile:94: recipe for target ‘mpi’ failed
make: *** [mpi] Error 2
I would really appreciate your help with this error.
After downloading and extracting the lammps (lammps-22 Aug-18 & lammps-10 Feb-15) tarball at the required location:
lammps>src and then use the command make mpi.
lammps>lib>kim. Extract kim-api-v1.6.0 at this location.
Download and extract Umeno model at lammps>lib>kim>kim-api-v1.6.0>src>models.
Follow the instructions mentioned in the INSTALL file to install at an alternative location.
cp Makefile.KIM_Config.example Makefile.KIM_Config
printf “g/^KIM_DIR/d\ni\nKIM_DIR = pwd\n.\nw\nq\n” | ed Makefile.KIM_Config
prefix=/path/to/alternate/location (I used prefix=/lammps/lib/kim/kim-api-v1.6.0)
printf “g/^#prefix/d\ni\nprefix = ${prefix}\n.\nw\nq\n” | ed Makefile.KIM_Config
make
make install
make install-set-default-to-v1
After downloading and extracting the lammps (lammps-22 Aug-18 & lammps-10 Feb-15) tarball at the required location:
lammps>lib>kim. Extract kim-api-v1.6.0 at this location.
Download and extract Umeno model at lammps>lib>kim>kim-api-v1.6.0>src>models.
Follow the instructions mentioned in the INSTALL file to install at an alternative location.
cp Makefile.KIM_Config.example Makefile.KIM_Config
printf “g/^KIM_DIR/d\ni\nKIM_DIR = pwd\n.\nw\nq\n” | ed Makefile.KIM_Config
prefix=/path/to/alternate/location (I used prefix=/lammps/lib/kim/kim-api-v1.6.0)
printf “g/^#prefix/d\ni\nprefix = ${prefix}\n.\nw\nq\n” | ed Makefile.KIM_Config
make
make install
make install-set-default-to-v1
Go to lammps>src. Then make lib-kim args=“-p /lammps/lib/kim/kim-api-v1.6.0”
Thank you for your help and quick response Ryan. I was able to build lammps following your instructions.
However, I am still having troubles using the Umeno model. The following is the lammps log file.
LAMMPS (23 Jun 2022 - Update 2)
Input file for uniaxial tensile loading of single crystal aluminum
Mark Tschopp, November 2010
------------------------ FORCE FIELDS ------------------------------
#pair_style eam/alloy #pair_coeff * * Al.eam.alloy Al
kim init Dipole_Umeno_YSZ__MO_394669891912_001 metal
#=== KIM is looking for ‘Portable Models’ in these directories ===
Hi,
Your latest message shows output from LAMMPS 23 Jun 2022. This can’t be the correct executable. You were working with LAMMPS 22 Aug-18 were you not?
My bad. I accidentally used the latest LAMMPS version instead of LAMMPS 22 Aug-18.
I followed your instructions and built LAMMPS 22 Aug-18, but when I tried to run the script, i got the following error message:
LAMMPS (22 Aug 2018)
Input file for uniaxial tensile loading of YSZ
Mark Tschopp, November 2010
------------------------ FORCE FIELDS ------------------------------
#pair_style eam/alloy #pair_coeff * * Al.eam.alloy Al
kim init Dipole_Umeno_YSZ__MO_394669891912_001 metal
ERROR: Unknown command: kim init Dipole_Umeno_YSZ__MO_394669891912_001 metal (…/input.cpp:246)
Last command: kim init Dipole_Umeno_YSZ__MO_394669891912_001 metal
Hi,
OK, something must not be going right during the various build commands.
Do you see any error messages as you build and install the kim-api? What about when you do the make lib-kim --args="..." command?
There were no error messages during the build and installation of kim-api. The following is the output after make lib-kim args=“-p /lammps/lib/kim/kim-api-v1.6.0”
(base) tejesh@tejesh-VirtualBox:~/Desktop/lammps-22Aug18/src$ make lib-kim args=“-p /Desktop/lammps-22Aug18/lib/kim/kim-api-v1.6.0”
Installing lib kim
Created /home/tejesh/Desktop/lammps-22Aug18/lib/kim/Makefile.KIM_DIR
using /Desktop/lammps-22Aug18/lib/kim/kim-api-v1.6.0
Please let me know if you know of any earlier LAMMPS versions that came with kim-api-v1.6.0.
Dear Dr. Relliott,
Thanks for your detailed explanation. I followed exactly the five steps given by you. Thanks to your help, I can run the examples/kim/in.kim.lj normally.
You are using “KIMvirial” in the pair_style line. The Dipole_Umeno_YSZ__MO_394669891912 model does not support this feature. Next, I would try replacing “KIMvirial” with “LAMMPSvirial”.
