Work in progress for extract_global; committing but will probably undo later
This commit is contained in:
Karl Hammond
@ -80,7 +80,7 @@ the optional logical argument set to ``.true.``. Here is a simple example:
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END PROGRAM testlib
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It is also possible to pass command line flags from Fortran to C/C++ and
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thus make the resulting executable behave similar to the standalone
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thus make the resulting executable behave similarly to the standalone
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executable (it will ignore the `-in/-i` flag, though). This allows to
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use the command line to configure accelerator and suffix settings,
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configure screen and logfile output, or to set index style variables
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@ -190,6 +190,7 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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:f reset_box: :f:func:`reset_box`
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:f memory_usage: :f:func:`memory_usage`
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:f extract_setting: :f:func:`extract_setting`
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:f extract_global: :f:func:`extract_global`
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--------
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@ -210,7 +211,57 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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:o integer comm [optional]: MPI communicator
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:r lammps: an instance of the :f:type:`lammps` derived type
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--------
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.. note::
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The ``MPI_F08`` module, which defines Fortran 2008 bindings for MPI,
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is not directly supported by this interface due to the complexities of
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supporting both the ``MPI_F08`` and ``MPI`` modules at the same time.
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However, you should be able to use the ``MPI_VAL`` member of the
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``MPI_comm`` derived type to access the integer value of the
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communicator, such as in
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.. code-block:: Fortran
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PROGRAM testmpi
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USE LIBLAMMPS
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USE MPI_F08
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TYPE(lammps) :: lmp
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lmp = lammps(MPI_COMM_SELF%MPI_VAL)
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END PROGRAM testmpi
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Constants Defined by the API
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============================
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The following constants are declared by the Fortran API to resolve the
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type/kind/rank signature for return values. These serve the same role as
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``LAMMPS_INT``, ``LAMMPS_DOUBLE``, and similar constants in ``src/library.h``
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and those in ``python/lammps/constants.py`` for the C and Python APIs,
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respectively. Unlike their C and Python bretheren, however, it is the type
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(e.g., ``INTEGER``), kind (e.g., ``C_int``), and rank (e.g., ``DIMENSION(:)``)
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of these constants that is used by the calling routine, rather than their
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numerical values.
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:f:LMP_INT: 32-bit integer scalars
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:f:LMP_INT_1D: 32-bit integer vectors
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:f:LMP_INT_2D: 32-bit integer matrices
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:f:LMP_DOUBLE: 64-bit real scalars
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:f:LMP_DOUBLE_1D: 64-bit real vectors
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:f:LMP_DOUBLE_2D: 64-bit real matrices
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:f:LMP_INT64: 64-bit integer scalars
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:f:LMP_INT64_1D: 64-bit integer vectors
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:f:LMP_INT64_2D: 64-bit integer matrices
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.. admonition:: Interaction with LAMMPS_BIGBIG and such
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LAMMPS uses different-sized integers to store various entities, such as
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the number of timesteps or the total number of atoms, depending on certain
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compiler flags (see the :doc:`size limits <Build_settings_size>`
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documentation). This API is currently agnostic to these settings, and it
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is up to the user to know the size of LAMMPS_BIGINT and such and pass
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LMP_INT or LMP_INT64, as appropriate, for such entities.
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Procedures Bound to the lammps Derived Type
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===========================================
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.. f:subroutine:: close([finalize])
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@ -278,6 +329,9 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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.. f:function:: get_thermo(name)
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This function will call :cpp:func:`lammps_get_thermo` and return the value
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of the corresponding thermodynamic keyword.
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:p character(len=*) name: string with the name of the thermo keyword
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:r real(C_double): value of the requested thermo property or 0.0_C_double
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@ -285,6 +339,11 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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.. f:subroutine:: extract_box(boxlo, boxhi, xy, yz, xz, pflags, boxflag)
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This subroutine will call :cpp:func:`lammps_extract_box`. All parameters
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are optional, though obviously at least one should be present. The
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parameters *pflags* and *boxflag* are stored in LAMMPS as integers, but
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should be declared as ``LOGICAL`` variables when calling from Fortran.
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:p real(c_double) boxlo [dimension(3),optional]: vector in which to store
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lower-bounds of simulation box
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:p real(c_double) boxhi [dimension(3),optional]: vector in which to store
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@ -302,6 +361,9 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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.. f:subroutine:: reset_box(boxlo, boxhi, xy, yz, xz)
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This subroutine will call :cpp:func:`lammps_reset_box`. All parameters
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are required.
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:p real(c_double) boxlo [dimension(3)]: vector of three doubles containing
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the lower box boundary
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:p real(c_double) boxhi [dimension(3)]: vector of three doubles containing
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@ -314,6 +376,9 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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.. f:subroutine:: memory_usage(meminfo)
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This subroutine will call :cpp:func:`lammps_memory_usage` and store the
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result in the three-element array *meminfo*.
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:p real(c_double) meminfo [dimension(3)]: vector of three doubles in which
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to store memory usage data
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@ -321,15 +386,25 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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.. f:function:: get_mpi_comm()
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This function returns a Fortran representation of the LAMMPS "world"
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communicator.
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:r integer: Fortran integer equivalent to the MPI communicator LAMMPS is
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using
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.. note::
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.. note::
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The MPI_F08 module, which is in compliance with the Fortran 2008 standard,
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is not directly supported by this function. However, you should be able to
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convert between the two using the MPI_VAL member of the communicator. For
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example,
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The C library interface currently returns type "int" instead of type
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"MPI_Fint", which is the C type correspending to Fortran "INTEGER"
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types of the default kind. On most compilers, these are the same anyway,
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but this interface exchanges values this way to avoid warning messages.
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.. note::
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The MPI_F08 module, which defines Fortran 2008 bindings for MPI, is not
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directly supported by this function. However, you should be able to
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convert between the two using the MPI_VAL member of the communicator.
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For example,
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.. code-block:: fortran
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@ -346,5 +421,57 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
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.. f:function:: extract_setting(keyword)
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Query LAMMPS about global settings. See the documentation for the
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:c:func:`lammps_extract_setting` function from the C library.
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:p character(len=*) keyword: string containing the name of the thermo keyword
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:r integer(c_int): value of the queried setting or :math:`-1` if unknown
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--------
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.. f:function:: extract_global(name, dtype)
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Overloaded function to get internal global LAMMPS data. Note that all
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currently implemented global types only return scalars or strings; all
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array-returning entities currently supported use :f:func:`extract_box`.
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Note that type/kind/rank of the *dtype* argument is used to determine
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whether to return a type correspending to a C int, a C int64_t, or a
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C double. The type/kind/rank signature of dtype is checked at runtime to
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match that of the return value; this type of check cannot be performed at
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compile time. For example,
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.. code-block:: fortran
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PROGRAM demo
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USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int64_t
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USE LIBLAMMPS
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TYPE(lammps) :: lmp
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INTEGER(C_int) :: nlocal
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INTEGER(C_int64_t) :: ntimestep
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CHARACTER(LEN=10) :: units
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REAL(C_double) :: dt
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lmp = lammps()
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! other commands
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nlocal = lmp%extract_global('nlocal', LMP_INT)
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ntimestep = lmp%extract_global('ntimestep', LMP_INT64)
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dt = lmp%extract_global('dt', LMP_DOUBLE)
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units = lmp%extract_global('units', LMP_STRING)
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! more commands
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lmp.close(.TRUE.)
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END PROGRAM demo
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would extract the number of atoms on this processor, the current time step,
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the size of the current time step, and the units being used into the
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variables *nlocal*, *ntimestep*, *dt*, and *units*, respectively.
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*Note*: if this function returns a string, the string must have
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length greater than or equal to the length of the string (not including the
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terminal NULL character) that LAMMPS returns. If the variable's length is
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too short, the string will be truncated. As usual in Fortran, strings
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are padded with spaces at the end.
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:p character(len=*) name: string with the name of the extracted property
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:p polymorphic dtype: one of *LMP_INT*, *LMP_INT64*, *LMP_DOUBLE*, or
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*LMP_STRING* designating the type/kind/rank of the return value
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:r polymorphic: value of the extracted property
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@ -38,10 +38,10 @@ MODULE LIBLAMMPS
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! These are public-interface constants that have the same purpose as the
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! constants in library.h, except that their types match the type of the
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! constant in question. Their purpose is to determine the type of the
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! constant in question. Their purpose is to specify the type of the
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! return value without something akin to a C/C++ type cast
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INTEGER (c_int), PUBLIC, PARAMETER :: LMP_INT = 0_c_int
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INTEGER (c_int), PUBLIC, DIMENSION(3), PARAMETER :: LMP_INT_1D = 1_c_int
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INTEGER (c_int), PUBLIC, DIMENSION(3), PARAMETER :: LMP_INT_1D = 0_c_int
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INTEGER (c_int), PUBLIC, DIMENSION(3,3), PARAMETER :: LMP_INT_2D = 1_c_int
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REAL (c_double), PUBLIC, PARAMETER :: LMP_DOUBLE = 2.0_c_double
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REAL (c_double), PUBLIC, DIMENSION(3), PARAMETER :: &
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@ -59,6 +59,8 @@ MODULE LIBLAMMPS
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!
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! Must be kept in sync with the equivalent declarations in
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! src/library.h and python/lammps/constants.py
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!
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! NOT part of the API (the part the user sees)
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INTEGER (c_int), PARAMETER :: &
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LAMMPS_INT = 0_c_int, & ! 32-bit integer (array)
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LAMMPS_INT_2D = 1, & ! two-dimensional 32-bit integer array
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@ -84,8 +86,12 @@ MODULE LIBLAMMPS
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PROCEDURE :: get_mpi_comm => lmp_get_mpi_comm
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PROCEDURE :: extract_setting => lmp_extract_setting
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PROCEDURE, PRIVATE :: lmp_extract_global_int
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GENERIC :: extract_global => lmp_extract_global_int ! TODO
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PROCEDURE, PRIVATE :: lmp_extract_global_int64_t
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PROCEDURE, PRIVATE :: lmp_extract_global_double
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PROCEDURE, PRIVATE :: lmp_extract_global_str
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GENERIC :: extract_global => lmp_extract_global_int, &
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lmp_extract_global_int64_t, lmp_extract_global_double, &
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lmp_extract_global_str
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PROCEDURE :: version => lmp_version
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END TYPE lammps
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@ -207,6 +213,13 @@ MODULE LIBLAMMPS
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INTEGER (c_int) :: lammps_extract_global_datatype
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END FUNCTION lammps_extract_global_datatype
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FUNCTION c_strlen (str) bind(C,name='strlen')
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IMPORT :: c_ptr, c_size_t
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IMPLICIT NONE
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TYPE(c_ptr) :: str
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INTEGER(c_size_t) :: c_strlen
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END FUNCTION c_strlen
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FUNCTION lammps_extract_global(handle, name) BIND(C)
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IMPORT :: c_ptr
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TYPE(c_ptr), VALUE :: handle, name
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@ -530,49 +543,94 @@ CONTAINS
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! END FUNCTION lmp_extract_global_datatype
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! equivalent functions to lammps_extract_global (overloaded)
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! This implementation assumes there are no non-scalar data that can be
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! extracted through lammps_extract_global
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FUNCTION lmp_extract_global_int (self, name, dtype)
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CLASS(lammps), INTENT(IN) :: self
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CHARACTER(LEN=*), INTENT(IN) :: name
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INTEGER(c_int) :: dtype
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INTEGER(c_int), INTENT(IN) :: dtype
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INTEGER(c_int) :: lmp_extract_global_int
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TYPE(c_ptr) :: Cname, Cptr
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INTEGER(c_int) :: datatype
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INTEGER(c_int), POINTER :: ptr
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Cname = f2c_string(name)
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datatype = lammps_extract_global_datatype(Cname)
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datatype = lammps_extract_global_datatype(c_null_ptr, Cname)
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IF ( datatype /= LAMMPS_INT ) THEN
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! throw an exception or something; data type doesn't match!
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WRITE(0,*) 'WARNING: global data type is inconsistent'
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WRITE(0,*) 'WARNING: global data type is inconsistent (not an int)'
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END IF
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Cptr = lammps_extract_global(self%handle, Cname)
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CALL c_f_pointer(Cptr, ptr)
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lmp_extract_global_int = ptr
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CALL lammps_free(Cname)
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END FUNCTION lmp_extract_global_int
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FUNCTION lmp_extract_global_int_1d (self, name, dtype)
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! This implementation assumes there are three elements to all arrays
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FUNCTION lmp_extract_global_int64_t (self, name, dtype)
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CLASS(lammps), INTENT(IN) :: self
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CHARACTER(LEN=*), INTENT(IN) :: name
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INTEGER(c_int), DIMENSION(3) :: dtype
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INTEGER(c_int) :: lmp_extract_global_int
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INTEGER(c_int64_t), INTENT(IN) :: dtype
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INTEGER(c_int64_t) :: lmp_extract_global_int64_t
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TYPE(c_ptr) :: Cname, Cptr
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INTEGER(c_int) :: datatype
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INTEGER(c_int), DIMENSION(3), POINTER :: ptr
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INTEGER(c_int64_t), POINTER :: ptr
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Cname = f2c_string(name)
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datatype = lammps_extract_global_datatype(Cname)
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IF ( datatype /= LAMMPS_INT ) THEN
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datatype = lammps_extract_global_datatype(c_null_ptr, Cname)
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IF ( datatype /= LAMMPS_INT64 ) THEN
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! throw an exception or something; data type doesn't match!
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WRITE(0,*) 'WARNING: global data type is inconsistent (not an int64_t)'
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END IF
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Cptr = lammps_extract_global(self%handle, Cname)
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CALL c_f_pointer(Cptr, ptr, shape(dtype))
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lmp_extract_global_int = ptr
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CALL c_f_pointer(Cptr, ptr)
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lmp_extract_global_int64_t = ptr
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CALL lammps_free(Cname)
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END FUNCTION lmp_extract_global_int_1d
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! TODO need more generics here to match TKR of LMP_INT_1D, LMP_BIGINT,
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! LMP_DOUBLE, LMP_DOUBLE_1D, LMS_STRING [this assumes no one adds anything
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! requiring LMP_DOUBLE_2D and the like!]
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END FUNCTION lmp_extract_global_int64_t
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FUNCTION lmp_extract_global_double (self, name, dtype)
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CLASS(lammps), INTENT(IN) :: self
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CHARACTER(LEN=*), INTENT(IN) :: name
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REAL(c_double), INTENT(IN) :: dtype
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REAL(c_double) :: lmp_extract_global_double
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TYPE(c_ptr) :: Cname, Cptr
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INTEGER(c_int) :: datatype
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REAL(c_double), POINTER :: ptr
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Cname = f2c_string(name)
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datatype = lammps_extract_global_datatype(c_null_ptr, Cname)
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IF ( datatype /= LAMMPS_DOUBLE ) THEN
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! throw an exception or something; data type doesn't match!
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WRITE(0,*) 'WARNING: global data type is inconsistent (not a double)'
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END IF
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Cptr = lammps_extract_global(self%handle, Cname)
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CALL c_f_pointer(Cptr, ptr)
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lmp_extract_global_double = ptr
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CALL lammps_free(Cname)
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END FUNCTION lmp_extract_global_double
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FUNCTION lmp_extract_global_str (self, name, dtype)
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CLASS(lammps), INTENT(IN) :: self
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CHARACTER(LEN=*), INTENT(IN) :: name, dtype
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CHARACTER(LEN=:), ALLOCATABLE :: lmp_extract_global_str
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TYPE(c_ptr) :: Cname, Cptr
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INTEGER(c_int) :: datatype
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CHARACTER(KIND=c_char,LEN=1), dimension(:), POINTER :: ptr
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INTEGER(c_size_t) :: length
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INTEGER :: i
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Cname = f2c_string(name)
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datatype = lammps_extract_global_datatype(c_null_ptr, Cname)
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IF ( datatype /= LAMMPS_STRING ) THEN
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! throw an exception or something; data type doesn't match!
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WRITE(0,*) 'WARNING: global data type is inconsistent (not a string)'
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END IF
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Cptr = lammps_extract_global(self%handle, Cname)
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length = c_strlen(Cptr)
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CALL c_f_pointer(Cptr, ptr, [length])
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ALLOCATE ( CHARACTER(LEN=length) :: lmp_extract_global_str )
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FORALL ( I=1:length )
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lmp_extract_global_str(i:i) = ptr(i)
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END FORALL
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CALL lammps_free(Cname)
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! the allocatable scalar (return value) gets auto-deallocated on return
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END FUNCTION lmp_extract_global_str
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! equivalent function to lammps_version()
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INTEGER FUNCTION lmp_version(self)
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Reference in New Issue
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