Loading doc/include-file-conventions.md +7 −4 Original line number Diff line number Diff line Loading @@ -3,7 +3,7 @@ This purpose of this document is to provide a point of reference for LAMMPS developers and contributors as to what include files and definitions to put where into LAMMPS source. Last change 2019-07-05 Last change 2020-08-31 ## Table of Contents Loading Loading @@ -99,10 +99,13 @@ Include files should be included in this order: #### pointers.h The `pointer.h` header file also includes `cstdio` and `lmptype.h` (and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`). The `pointer.h` header file also includes `cstdio`, `cstddef`, `string`, `lmptype.h`, and `utils.h` (and through those indirectly `stdint.h`, `intttypes.h`, cstdlib, and `climits`). This means any header including `pointers.h` can assume that `FILE`, `NULL`, `INT_MAX` are defined. `NULL`, `INT_MAX` are defined, they may freely use std::string and functions from the utils namespace without including the corresponding header files. ## Tools Loading doc/src/Install_linux.rst +3 −3 Original line number Diff line number Diff line Loading @@ -79,13 +79,13 @@ To get a copy of the current potentials files: which will download the potentials files to ``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is hard-coded to look for potential files in this directory (it does not use the `LAMMPS_POTENTIALS` environment variable, as described use the ``LAMMPS_POTENTIALS`` environment variable, as described in :doc:`pair_coeff <pair_coeff>` command). The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which results in the above command also installing the `kim-api` binaries when LAMMPS results in the above command also installing the ``kim-api`` binaries when LAMMPS is installed. In order to use potentials from `openkim.org <openkim_>`_, you can install the `openkim-models` package can install the ``openkim-models`` package .. code-block:: bash Loading doc/src/pair_coeff.rst +7 −2 Original line number Diff line number Diff line Loading @@ -110,8 +110,8 @@ location specified. E.g. if the file is specified as "niu3.eam", it is looked for in the current working directory. If it is specified as "../potentials/niu3.eam", then it is looked for in the potentials directory, assuming it is a sister directory of the current working directory. If the file is not found, it is then looked for in the directory specified by the LAMMPS_POTENTIALS environment variable. directory. If the file is not found, it is then looked for in one of the directories specified by the ``LAMMPS_POTENTIALS`` environment variable. Thus if this is set to the potentials directory in the LAMMPS distribution, then you can use those files from anywhere on your system, without copying them into your working directory. Environment variables are Loading @@ -136,6 +136,11 @@ Windows: % set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials" The ``LAMMPS_POTENTIALS`` environment variable may contain paths to multiple folders, if they are separated by ";" on Windows and ":" on all other operating systems, just like the ``PATH`` and similar environment variables. ---------- The alphabetic list of pair styles defined in LAMMPS is given on the Loading doc/src/pair_comb.rst +2 −2 Original line number Diff line number Diff line Loading @@ -129,10 +129,10 @@ For style *comb3*\ , in addition to ffield.comb3, a special parameter file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be automatically loaded if carbon atom is detected in LAMMPS input structure. This file must be in your working directory or in the directory pointed to by the environment variable LAMMPS_POTENTIALS, as directories listed in the environment variable ``LAMMPS_POTENTIALS``, as described on the :doc:`pair_coeff <pair_coeff>` command doc page. Keyword *polar* indicates whether the force field includes The keyword *polar* indicates whether the force field includes the atomic polarization. Since the equilibration of the polarization has not yet been implemented, it can only set polar_off at present. Loading doc/src/pair_python.rst +6 −6 Original line number Diff line number Diff line Loading @@ -38,12 +38,12 @@ corresponding compiled code. This penalty can be significantly reduced through generating tabulations from the python code through the :doc:`pair_write <pair_write>` command, which is supported by this style. Only a single pair_coeff command is used with the *python* pair style which specifies a python class inside a python module or file that LAMMPS will look up in the current directory, the folder pointed to by the LAMMPS_POTENTIALS environment variable or somewhere in your python path. A single python module can hold multiple python pair class definitions. The class definitions itself have to follow specific Only a single :doc:`pair_coeff <pair_coeff>` command is used with the *python* pair style which specifies a python class inside a python module or a file that LAMMPS will look up in the current directory, a folder pointed to by the ``LAMMPS_POTENTIALS`` environment variable or somewhere in your python path. A single python module can hold multiple python pair class definitions. The class definitions itself have to follow specific rules that are explained below. Atom types in the python class are specified through symbolic Loading Loading
doc/include-file-conventions.md +7 −4 Original line number Diff line number Diff line Loading @@ -3,7 +3,7 @@ This purpose of this document is to provide a point of reference for LAMMPS developers and contributors as to what include files and definitions to put where into LAMMPS source. Last change 2019-07-05 Last change 2020-08-31 ## Table of Contents Loading Loading @@ -99,10 +99,13 @@ Include files should be included in this order: #### pointers.h The `pointer.h` header file also includes `cstdio` and `lmptype.h` (and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`). The `pointer.h` header file also includes `cstdio`, `cstddef`, `string`, `lmptype.h`, and `utils.h` (and through those indirectly `stdint.h`, `intttypes.h`, cstdlib, and `climits`). This means any header including `pointers.h` can assume that `FILE`, `NULL`, `INT_MAX` are defined. `NULL`, `INT_MAX` are defined, they may freely use std::string and functions from the utils namespace without including the corresponding header files. ## Tools Loading
doc/src/Install_linux.rst +3 −3 Original line number Diff line number Diff line Loading @@ -79,13 +79,13 @@ To get a copy of the current potentials files: which will download the potentials files to ``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is hard-coded to look for potential files in this directory (it does not use the `LAMMPS_POTENTIALS` environment variable, as described use the ``LAMMPS_POTENTIALS`` environment variable, as described in :doc:`pair_coeff <pair_coeff>` command). The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which results in the above command also installing the `kim-api` binaries when LAMMPS results in the above command also installing the ``kim-api`` binaries when LAMMPS is installed. In order to use potentials from `openkim.org <openkim_>`_, you can install the `openkim-models` package can install the ``openkim-models`` package .. code-block:: bash Loading
doc/src/pair_coeff.rst +7 −2 Original line number Diff line number Diff line Loading @@ -110,8 +110,8 @@ location specified. E.g. if the file is specified as "niu3.eam", it is looked for in the current working directory. If it is specified as "../potentials/niu3.eam", then it is looked for in the potentials directory, assuming it is a sister directory of the current working directory. If the file is not found, it is then looked for in the directory specified by the LAMMPS_POTENTIALS environment variable. directory. If the file is not found, it is then looked for in one of the directories specified by the ``LAMMPS_POTENTIALS`` environment variable. Thus if this is set to the potentials directory in the LAMMPS distribution, then you can use those files from anywhere on your system, without copying them into your working directory. Environment variables are Loading @@ -136,6 +136,11 @@ Windows: % set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials" The ``LAMMPS_POTENTIALS`` environment variable may contain paths to multiple folders, if they are separated by ";" on Windows and ":" on all other operating systems, just like the ``PATH`` and similar environment variables. ---------- The alphabetic list of pair styles defined in LAMMPS is given on the Loading
doc/src/pair_comb.rst +2 −2 Original line number Diff line number Diff line Loading @@ -129,10 +129,10 @@ For style *comb3*\ , in addition to ffield.comb3, a special parameter file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be automatically loaded if carbon atom is detected in LAMMPS input structure. This file must be in your working directory or in the directory pointed to by the environment variable LAMMPS_POTENTIALS, as directories listed in the environment variable ``LAMMPS_POTENTIALS``, as described on the :doc:`pair_coeff <pair_coeff>` command doc page. Keyword *polar* indicates whether the force field includes The keyword *polar* indicates whether the force field includes the atomic polarization. Since the equilibration of the polarization has not yet been implemented, it can only set polar_off at present. Loading
doc/src/pair_python.rst +6 −6 Original line number Diff line number Diff line Loading @@ -38,12 +38,12 @@ corresponding compiled code. This penalty can be significantly reduced through generating tabulations from the python code through the :doc:`pair_write <pair_write>` command, which is supported by this style. Only a single pair_coeff command is used with the *python* pair style which specifies a python class inside a python module or file that LAMMPS will look up in the current directory, the folder pointed to by the LAMMPS_POTENTIALS environment variable or somewhere in your python path. A single python module can hold multiple python pair class definitions. The class definitions itself have to follow specific Only a single :doc:`pair_coeff <pair_coeff>` command is used with the *python* pair style which specifies a python class inside a python module or a file that LAMMPS will look up in the current directory, a folder pointed to by the ``LAMMPS_POTENTIALS`` environment variable or somewhere in your python path. A single python module can hold multiple python pair class definitions. The class definitions itself have to follow specific rules that are explained below. Atom types in the python class are specified through symbolic Loading
