Description:
-This pair style is a wrapper on the Knowledge Base for Interatomic
+ This pair style is a wrapper on the Knowledge Base for Interatomic
Models (KIM) repository of interatomic potentials,
so that they can be used by LAMMPS scripts.
The argument virialmode determines how the global virial is calculated. If KIMvirial is specified, the KIM model performs the -global virial calculation. If LAMMPSvirial is specified, LAMMPS -computes the global virial using its fdotr mechanism. +global virial calculation (if it knows how). If LAMMPSvirial is +specified, LAMMPS computes the global virial using its fdotr mechanism.
The argument model is the name of the KIM model for a specific potential as KIM defines it. In principle, LAMMPS can invoke any KIM @@ -76,174 +76,118 @@ directory where LAMMPS is running.
Here is information on how to build KIM for use with LAMMPS. There is -a directory src/KIM/ with an important file in it: Makefile.lammps. -When you do 'make yes-kim' LAMMPS will use the settings in -src/KIM/Makefile.lammps to find KIM header files and the KIM library -itself for linking purposes. Thus, you should ensure Makefile.lammps -has the correct settings for your system and your build of KIM. +
Here is information on how to build KIM for use with LAMMPS.
-Consult the KIM documentation for further details on KIM specifics. -
-OpenKIM is available for download from this site, -namely http://openkim.org. The tarball you download is -"openkim-api-vX.X.X.tgz", which can be unpacked via +
The KIM API is available for download from this +site, namely https://openkim.org. The tarball +you download is "openkim-api-vX.X.X.tgz", which can be unpacked via
tar xvfz openkim*tgz-
The openkim-api-vX.X.X/DOCS directory has further documentation. For -more information on installing KIM and troubleshooting refer to -openkim/INSTALL. +
The openkim-api-vX.X.X/DOCS/ directory has further documentation. In +order to compile and install the KIM API follow the instructions found +in the file openkim-api-vX.X.X/INSTALL. (Don't forget to download and +compile any Model Drivers and Models that you want to use.)
-Here is a brief summary of how to build KIM: +
Once you have successfully compiled and installed the KIM API, you +need to set up LAMMPS to use your KIM API system. In the LAMMPS +package there is a directory src/KIM/ with an important file in it: +Makefile.lammps. When you do 'make yes-kim' LAMMPS will use the +settings in src/KIM/Makefile.lammps to find the KIM API header files +and the KIM API library itself for linking purposes. Thus, you should +edit src/KIM/Makefile.lammps to ensure it has the correct settings for +your system and your build of KIM.
-The following is an example of how to download, compile, and run +LAMMPS with the KIM API: +
++mkdir lammps-kim +cd lammps-kim -
(a) Copy the file Makefile.KIM_Config.example to Makefile.KIM_Config - For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in - your home directory, you would do: --
% cd $HOME/openkim-api-vX.X.X - % cp Makefile.KIM_Config.example Makefile.KIM_Config --
The `%' symbol represents the bash sell prompt and should not be typed. - --
(Above `vX.X.X' represents the current release number.) --
(b) Edit the file Makefile.KIM_Config and set the appropriate value for the - KIM_DIR variable. This must expand to an absolute path. Using the same - assumptions as above, this would be --
KIM_DIR = $(HOME)/openkim-api-vX.X.X --
(c) If appropriate, set explicit values for the remaining three - directories --
KIM_MODEL_DRIVERS_DIR = - KIM_MODELS_DIR = - KIM_TESTS_DIR = --
If these lines are commented out, defaults will be provided by the - openkim-api make system. --
(d) Set the value of KIM_COMPILERSUITE. Possible values are `GCC' and - `INTEL'. --
KIM_COMPILERSUITE = GCC --
(e) Set the value of KIM_SYSTEMLINKER. Possible values are `linux', - `freebsd', and `darwin'. --
KIM_SYSTEMLINKER = linux --
(f) Set the value of KIM_SYSTEMARCH. Possible values are `32bit' and - `64bit'. --
KIM_SYSTEMARCH = 64bit --
(g) Set the value of KIM_LINK. Possible values are `dynamic-load', - `dynamic-link', and `static-link'. --
KIM_LINK = dynamic-load --
`dynamic-load' is the preferred option. (Unless performance or - other issues require it, you should use dynamic-load.) - `dynamic-link' is like `dynamic-load' but does not use the dl.h - library. This option requires a more complicated Makefile - process, but may improve computation time in some instances. - `static-link' only works with ONE Model and AT MOST ONE Model - Driver (in order to avoid the possibility of symbol - clashes). --
(h) Set override values for other variables, if necessary, by - adding the desired variable name (after the "# overwrite - default variable values here" line) and filling in appropriate - values. --
# overwrite default variable values here --
# overwrite default compiler options --
CC = - CXX = - FC = --
# overwrite default compiler option flag lists - FFLAGS = - CCFLAGS = - CXXFLAGS = - LDFLAGS = --
# overwrite default linker options - LDSHAREDFLAG = - LINKSONAME = - LDWHOLEARCHIVESTARTFLAG = - LDWHOLEARCHIVEENDFLAG = --
# overwrite default install directories - package_name = - prefix = - libdir = --
bash: - % export KD=$HOME/openkim-api-vX.X.X --
% cd $KD - % make examples - % make --
This builds all Model Drivers, Models, Tests, and the openkim-api service - routine library. The targets defined by the Makefile in this directory - include: --
`make' -- compiles the API and all Models and Tests - `make all' -- same as `make' - `make clean' -- will remove appropriate .o, .mod, .a, .so and - executable files - `make install' -- install files to `/usr/local/lib' by default - `make uninstall' -- delete files installed by `make install' - `make openkim-api' -- compiles only the API - `make examples' -- copies examples into the appropriate - directories (no overwrite) - `make examples-force' -- copies examples into the appropriate - directories (overwrite) - `make examples-clean' -- remove all examples from the MODEL_DRIVERS, - MODELS, and TESTS directories. --
The provided example Tests read in the name of a Model (or Models) - which they use to perform their calculations. For most Tests the - name of the Model can be piped in using an `echo' command. For - example, the following Fortran 90 Test reads in one Model: --
% cd $KD/TESTs/test_Ar_free_cluster_CLUSTER_F90 - % echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90 --
(See the README files in the Test directories for an explanation of what - the Tests do.) --
Mixing, shift, table, tail correction, restart, rRESPA info: diff --git a/doc/pair_kim.txt b/doc/pair_kim.txt index 59b57810a9..0d30d50a14 100644 --- a/doc/pair_kim.txt +++ b/doc/pair_kim.txt @@ -23,7 +23,7 @@ pair_coeff * * Ar Ar :pre [Description:] This pair style is a wrapper on the "Knowledge Base for Interatomic -Models (KIM)"_http://openkim.org repository of interatomic potentials, +Models (KIM)"_https://openkim.org repository of interatomic potentials, so that they can be used by LAMMPS scripts. In KIM lingo, a potential is a "model" and a model contains both the @@ -33,8 +33,8 @@ cutoffs. The argument {virialmode} determines how the global virial is calculated. If {KIMvirial} is specified, the KIM model performs the -global virial calculation. If {LAMMPSvirial} is specified, LAMMPS -computes the global virial using its fdotr mechanism. +global virial calculation (if it knows how). If {LAMMPSvirial} is +specified, LAMMPS computes the global virial using its fdotr mechanism. The argument {model} is the name of the KIM model for a specific potential as KIM defines it. In principle, LAMMPS can invoke any KIM @@ -73,172 +73,116 @@ directory where LAMMPS is running. :line -Here is information on how to build KIM for use with LAMMPS. There is -a directory src/KIM/ with an important file in it: Makefile.lammps. -When you do 'make yes-kim' LAMMPS will use the settings in -src/KIM/Makefile.lammps to find KIM header files and the KIM library -itself for linking purposes. Thus, you should ensure Makefile.lammps -has the correct settings for your system and your build of KIM. +Here is information on how to build KIM for use with LAMMPS. -Consult the KIM documentation for further details on KIM specifics. - -OpenKIM is available for download from "this site"_http://openkim.org, -namely http://openkim.org. The tarball you download is -"openkim-api-vX.X.X.tgz", which can be unpacked via +The KIM API is available for download from "this +site"_https://openkim.org, namely https://openkim.org. The tarball +you download is "openkim-api-vX.X.X.tgz", which can be unpacked via tar xvfz openkim*tgz :pre -The openkim-api-vX.X.X/DOCS directory has further documentation. For -more information on installing KIM and troubleshooting refer to -openkim/INSTALL. +The openkim-api-vX.X.X/DOCS/ directory has further documentation. In +order to compile and install the KIM API follow the instructions found +in the file openkim-api-vX.X.X/INSTALL. (Don't forget to download and +compile any Model Drivers and Models that you want to use.) -Here is a brief summary of how to build KIM: +Once you have successfully compiled and installed the KIM API, you +need to set up LAMMPS to use your KIM API system. In the LAMMPS +package there is a directory src/KIM/ with an important file in it: +Makefile.lammps. When you do 'make yes-kim' LAMMPS will use the +settings in src/KIM/Makefile.lammps to find the KIM API header files +and the KIM API library itself for linking purposes. Thus, you should +edit src/KIM/Makefile.lammps to ensure it has the correct settings for +your system and your build of KIM. -If you have previously used the openkim-api package (versions 1.1.1 or -below), it is recommended that you remove all associated environment -variables from your environment. (These include, KIM_DIR, KIM_INTEL, -KIM_SYSTEM32, KIM_DYNAMIC, KIM_API_DIR, KIM_TESTS_DIR, -KIM_MODEL_DRIVERS_DIR, and KIM_MODELS_DIR.) All setting are now -specified in the Makefile.KIM_Config file. :olb,l +The following is an example of how to download, compile, and run +LAMMPS with the KIM API: -Set up the Makefile.KIM_Config file :l +
+mkdir lammps-kim
+cd lammps-kim :
- (a) Copy the file Makefile.KIM_Config.example to Makefile.KIM_Config
- For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in
- your home directory, you would do: :pre
+#
+# download lammps and the KIM API
+# :
- % cd $HOME/openkim-api-vX.X.X
- % cp Makefile.KIM_Config.example Makefile.KIM_Config :pre
+wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
+wget http://s3.openkim.org/openkim-api/openkim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
+tar zxvf openkim-api-vX.X.X.tgz :
- The `%' symbol represents the bash sell prompt and should not be typed.
- :pre
+#
+# Get OpenKIM models, setup and compile
+# :
- (Above `vX.X.X' represents the current release number.) :pre
+cd openkim-api-vX.X.X
+cp Makefile.KIM_Config.example Makefile.KIM_Config
+vi Makefile.KIM_Config # edit file as appropriate following the instructions given in the INSTALL file
+cd MODEL_DRIVERS
+wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo__MD_120291908751_000&compression=gz'
+tar zxvf EAM_Dynamo__MD_120291908751_000.tgz
+cd ../MODELS
+wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000&compression=gz'
+tar zxvf EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000.tgz
+cd ../
+make
+cd ../ :
- (b) Edit the file Makefile.KIM_Config and set the appropriate value for the
- KIM_DIR variable. This must expand to an absolute path. Using the same
- assumptions as above, this would be :pre
+#
+# setup and compile lammps
+# :
- KIM_DIR = $(HOME)/openkim-api-vX.X.X :pre
+tar zxvf lammps-DDMMMYY.tar.gz
+cd lammps-DDMMMYY/src/KIM
+vi Makefile.lammps # edit the three lines to look like below:
+ # kim_SYSINC = -I../../../openkim-api-vX.X.X/KIM_API
+ # kim_SYSLIB = -lkim
+ # kim_SYSPATH = -L../../../openkim-api-vX.X.X/KIM_API
+cd ../
+make yes-kim
+cd STUBS
+make
+cd ../
+make serial :
- (c) If appropriate, set explicit values for the remaining three
- directories :pre
+#
+# run simple example with KIM model
+# :
- KIM_MODEL_DRIVERS_DIR =
- KIM_MODELS_DIR =
- KIM_TESTS_DIR = :pre
+cd ../../
+vi al-input # create file with the following content
+#----------------------------------------------------------------------------------------
+variable x index 1
+variable y index 1
+variable z index 1 :
- If these lines are commented out, defaults will be provided by the
- openkim-api make system. :pre
+variable xx equal 20*$x
+variable yy equal 20*$y
+variable zz equal 20*$z :
- (d) Set the value of KIM_COMPILERSUITE. Possible values are `GCC' and
- `INTEL'. :pre
+units metal
+atom_style atomic :
- KIM_COMPILERSUITE = GCC :pre
+lattice fcc 4.0500
+region box block 0.0 $\{xx\} 0.0 $\{yy\} 0.0 $\{zz\}
+create_box 1 box
+create_atoms 1 box :
- (e) Set the value of KIM_SYSTEMLINKER. Possible values are `linux',
- `freebsd', and `darwin'. :pre
+pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000
+pair_coeff * * Al :
- KIM_SYSTEMLINKER = linux :pre
+mass 1 26.98
+velocity all create 200.0 232345 loop geom :
- (f) Set the value of KIM_SYSTEMARCH. Possible values are `32bit' and
- `64bit'. :pre
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes :
- KIM_SYSTEMARCH = 64bit :pre
+fix 1 all nve :
- (g) Set the value of KIM_LINK. Possible values are `dynamic-load',
- `dynamic-link', and `static-link'. :pre
+run 100
+#---------------------------------------------------------------------------------------- :
- KIM_LINK = dynamic-load :pre
-
- `dynamic-load' is the preferred option. (Unless performance or
- other issues require it, you should use dynamic-load.)
- `dynamic-link' is like `dynamic-load' but does not use the dl.h
- library. This option requires a more complicated Makefile
- process, but may improve computation time in some instances.
- `static-link' only works with ONE Model and AT MOST ONE Model
- Driver (in order to avoid the possibility of symbol
- clashes). :pre
-
- (h) Set override values for other variables, if necessary, by
- adding the desired variable name (after the "# overwrite
- default variable values here" line) and filling in appropriate
- values. :pre
-
- # overwrite default variable values here :pre
-
- # overwrite default compiler options :pre
- CC =
- CXX =
- FC = :pre
-
- # overwrite default compiler option flag lists
- FFLAGS =
- CCFLAGS =
- CXXFLAGS =
- LDFLAGS = :pre
-
- # overwrite default linker options
- LDSHAREDFLAG =
- LINKSONAME =
- LDWHOLEARCHIVESTARTFLAG =
- LDWHOLEARCHIVEENDFLAG = :pre
-
- # overwrite default install directories
- package_name =
- prefix =
- libdir = :pre
-
-In the remainder of the documentation we will use the string $KD to
-represent the location of the openkim-api source package (the value of
-the KIM_DIR variable discussed above). If you wish to, type the below
-commands exactly as written to set the shell variable KD to the
-appropriate value: :l
-
- bash:
- % export KD=$HOME/openkim-api-vX.X.X :pre
-
-To compile the package, including the provided examples, change to the
-$KD directory and execute `make examples' and then `make': :l
-
- % cd $KD
- % make examples
- % make :pre
-
- This builds all Model Drivers, Models, Tests, and the openkim-api service
- routine library. The targets defined by the Makefile in this directory
- include: :pre
-
- `make' -- compiles the API and all Models and Tests
- `make all' -- same as `make'
- `make clean' -- will remove appropriate .o, .mod, .a, .so and
- executable files
- `make install' -- install files to `/usr/local/lib' by default
- `make uninstall' -- delete files installed by `make install'
- `make openkim-api' -- compiles only the API
- `make examples' -- copies examples into the appropriate
- directories (no overwrite)
- `make examples-force' -- copies examples into the appropriate
- directories (overwrite)
- `make examples-clean' -- remove all examples from the MODEL_DRIVERS,
- MODELS, and TESTS directories. :pre
-
-Verify that the compilation was successful by running a Test. :l
-
- The provided example Tests read in the name of a Model (or Models)
- which they use to perform their calculations. For most Tests the
- name of the Model can be piped in using an `echo' command. For
- example, the following Fortran 90 Test reads in one Model: :pre
-
- % cd $KD/TESTs/test_Ar_free_cluster_CLUSTER_F90
- % echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90 :pre
-
- (See the README files in the Test directories for an explanation of what
- the Tests do.) :pre
-
-Each Test (and Model) has its own make file for compiling and linking.
-If changes are made to the code, re-compile (from the $KD
-directory). :l,ole
+./lammps-DDMMYY/src/lmp_serial < al-input :
+
:line