Error adding YSZ model

techdube · January 25, 2023, 5:07pm

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!

relliott · January 27, 2023, 6:09pm

Hello,

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.

Best,

Ryan

techdube · January 30, 2023, 9:08pm

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.

Thank you for your time.

Best
Tejesh

relliott · January 30, 2023, 10:38pm

Hello,

I think I’ll need more details about all the commands you are using to set this all up, so that I can reproduce it if I need to.

Thanks,

Ryan

techdube · January 31, 2023, 5:55pm

Sure!

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

Go to lammps>src. Then make yes-KIM
make mpi.

Thank you for your help.

Best
Tejesh

relliott · January 31, 2023, 8:05pm

Hi,
OK. Try this instead:

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”
make mpi.

techdube · January 31, 2023, 9:35pm

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 ===

1: .

2: /home/tejesh/.kim-api/2.3.0+GNU.GNU.GNU.2023-01-18-21-01-03/portable-models-dir

3: /usr/local/lib/pkgconfig/…/…//lib/kim-api/portable-models

#=== KIM is looking for ‘Simulator Models’ in these directories ===

1: .

2: /home/tejesh/.kim-api/2.3.0+GNU.GNU.GNU.2023-01-18-21-01-03/simulator-models-dir

3: /usr/local/lib/pkgconfig/…/…//lib/kim-api/simulator-models

ERROR: KIM Model name not found (…/kim_init.cpp:234)

Last command: kim init Dipole_Umeno_YSZ__MO_394669891912_001 metal

relliott · February 1, 2023, 4:31am

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?

Ryan

techdube · February 1, 2023, 7:28pm

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

Following this I checked for the installed packages and found out that Kim wasn’t installed.
(base) tejesh@tejesh-VirtualBox:~/Desktop/lammps-22Aug18/src$ make ps
Installed NO: package ASPHERE
Installed NO: package BODY
Installed NO: package CLASS2
Installed NO: package COLLOID
Installed NO: package COMPRESS
Installed NO: package CORESHELL
Installed NO: package DIPOLE
Installed NO: package GPU
Installed NO: package GRANULAR
Installed NO: package KIM
Installed NO: package KOKKOS
Installed NO: package KSPACE
Installed NO: package LATTE
Installed NO: package MANYBODY
Installed NO: package MC
Installed NO: package MEAM
Installed NO: package MISC
Installed NO: package MOLECULE
Installed NO: package MPIIO
Installed NO: package MSCG
Installed NO: package OPT
Installed NO: package PERI
Installed NO: package POEMS
Installed NO: package PYTHON
Installed NO: package QEQ
Installed NO: package REAX
Installed NO: package REPLICA
Installed NO: package RIGID
Installed NO: package SHOCK
Installed NO: package SNAP
Installed NO: package SPIN
Installed NO: package SRD
Installed NO: package VORONOI

Installed NO: package USER-ATC
Installed NO: package USER-AWPMD
Installed NO: package USER-BOCS
Installed NO: package USER-CGDNA
Installed NO: package USER-CGSDK
Installed NO: package USER-COLVARS
Installed NO: package USER-DIFFRACTION
Installed NO: package USER-DPD
Installed NO: package USER-DRUDE
Installed NO: package USER-EFF
Installed NO: package USER-FEP
Installed NO: package USER-H5MD
Installed NO: package USER-INTEL
Installed NO: package USER-LB
Installed NO: package USER-MANIFOLD
Installed NO: package USER-MEAMC
Installed NO: package USER-MESO
Installed NO: package USER-MGPT
Installed NO: package USER-MISC
Installed NO: package USER-MOFFF
Installed NO: package USER-MOLFILE
Installed NO: package USER-NETCDF
Installed NO: package USER-OMP
Installed NO: package USER-PHONON
Installed NO: package USER-QMMM
Installed NO: package USER-QTB
Installed NO: package USER-QUIP
Installed NO: package USER-REAXC
Installed NO: package USER-SMD
Installed NO: package USER-SMTBQ
Installed NO: package USER-SPH
Installed NO: package USER-TALLY
Installed NO: package USER-UEF
Installed NO: package USER-VTK

I then tried make yes-KIM and make mpi but still got the same error message.
Please advise.

Thank you for your time and help.

Best
Tejesh

relliott · February 1, 2023, 8:37pm

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?

Ryan

techdube · February 1, 2023, 9:59pm

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.

Thank you for your help.

Best
Tejesh

relliott · February 1, 2023, 10:48pm

Instead of

make lib-kim args=“-p /Desktop/lammps-22Aug18/lib/kim/kim-api-v1.6.0”

try

make lib-kim args=“-p /home/tejesh/Desktop/lammps-22Aug18/lib/kim/kim-api-v1.6.0”