Finished docs for everything currently implemented
This commit is contained in:
Karl Hammond
@ -649,7 +649,40 @@ Procedures Bound to the lammps Derived Type
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will print the *y*-coordinate of the sixth atom on this processor
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(note the transposition of the two indices). This is not a choice, but
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rather a consequence of the different conventions adopted by the Fortran
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and C standards decades ago.
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and C standards decades ago: in C, the block of data
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.. parsed-literal::
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
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interpreted as a :math:`4\times4` matrix would be
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.. math::
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\begin{bmatrix}
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1 & 2 & 3 & 4 \\
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5 & 6 & 7 & 8 \\
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9 & 10 & 11 & 12 \\
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13 & 14 & 15 & 16
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\end{bmatrix},
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that is, in row-major order. In Fortran, the same block of data is
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interpreted in column-major order, namely,
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.. math::
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\begin{bmatrix}
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1 & 5 & 9 & 13 \\
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2 & 6 & 10 & 14 \\
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3 & 7 & 11 & 15 \\
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4 & 8 & 12 & 16
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\end{bmatrix}.
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This difference in interpretation of the same block of data by the two
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languages means, in effect, that matrices from C or C++ will be
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transposed when interpreted in Fortran.
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.. note::
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If you would like the indices to start at 0 instead of 1 (which follows
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typical notation in C and C++, but not Fortran), you can create another
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@ -776,7 +809,7 @@ Procedures Bound to the lammps Derived Type
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--------
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.. f:function:: extract_fix(id, style, type, [nrow,] [ncol])
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.. f:function:: extract_fix(id, style, type[, nrow][, ncol])
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This function calls :c:func:`lammps_extract_fix` and returns a pointer to
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LAMMPS data tied to the :cpp:class:`Fix` class, specifically data provided
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@ -884,7 +917,9 @@ Procedures Bound to the lammps Derived Type
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be of type ``REAL(C_double)`` and have appropriate rank (i.e.,
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``DIMENSION(:)`` if expecting per-atom or local vector data and
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``DIMENSION(:,:)`` if expecting per-atom or local array data). If expecting
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global or per-atom data, it should have the ``POINTER`` attribute.
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local or per-atom data, it should have the ``POINTER`` attribute, but
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if expecting global data, it should be an ordinary (non-``POINTER``)
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variable.
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.. admonition:: Array index order
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@ -970,26 +1005,72 @@ Procedures Bound to the lammps Derived Type
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.. f:subroutine:: flush_buffers
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..
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TODO
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This function calls :cpp:func:`lammps_flush_buffers`, which flushes buffered
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output to be written to screen and logfile. This can simplify capturing
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output from LAMMPS library calls.
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.. versionadded:: TBD
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--------
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.. f:function:: is_running
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..
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TODO
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Check if LAMMPS is currently inside a run or minimization.
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.. versionadded:: TBD
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This function can be used from signal handlers or multi-threaded
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applications to determine if the LAMMPS instance is currently active.
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:r logical: ``.FALSE.`` if idle or ``.TRUE.`` if active
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--------
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.. f:function:: has_error
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..
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TODO
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Check if there is a (new) error message available.
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.. versionadded:: TBD
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This function can be used to query if an error inside of LAMMPS
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has thrown a :ref:`C++ exception <exceptions>`.
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.. note::
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This function will always report "no error" when the LAMMPS library
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has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
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errors aborting LAMMPS into C++ exceptions. You can use the library
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function :cpp:func:`lammps_config_has_exceptions` to check if this is
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the case.
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:r logical: ``.TRUE.`` if there is an error.
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--------
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.. f:subroutine:: get_last_error_message
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.. f:subroutine:: get_last_error_message(buffer[,status])
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..
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TODO
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Copy the last error message into the provided buffer.
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.. versionadded:: TBD
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This function can be used to retrieve the error message that was set
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in the event of an error inside of LAMMPS that resulted in a
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:ref:`C++ exception <exceptions>`. A suitable buffer for a string has
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to be provided. If the internally-stored error message is longer than the
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string and the string does not have ``ALLOCATABLE`` length, it will be
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truncated accordingly. The optional argument *status* indicates the
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kind of error: a "1" indicates an error that occurred on all MPI ranks and
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is often recoverable, while a "2" indicates an abort that would happen only
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in a single MPI rank and thus may not be recoverable, as other MPI ranks may
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be waiting on the failing MPI rank(s) to send messages.
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.. note::
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This function will do nothing when the LAMMPS library has been
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compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
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LAMMPS into C++ exceptions. You can use the function
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:f:func:`config_has_exceptions` to check whethher this is the case.
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:p character(len=\*) buffer: string buffer to copy the error message into
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:o integer(C_int) status [optional]: 1 when all ranks had the error,
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2 on a single-rank error.
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@ -6,6 +6,7 @@ fixes, or variables in LAMMPS using the following functions:
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- :cpp:func:`lammps_extract_compute`
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- :cpp:func:`lammps_extract_fix`
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- :cpp:func:`lammps_extract_variable_datatype`
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- :cpp:func:`lammps_extract_variable`
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- :cpp:func:`lammps_set_variable`
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@ -2139,7 +2139,7 @@ with the specified name. See :cpp:enum:`_LMP_VAR_CONST` for valid values.
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Callers of :cpp:func:`lammps_extract_variable` can use this information to
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decide how to cast the (void*) pointer and access the data.
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..versionadded:: TBD
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.. versionadded:: TBD
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\endverbatim
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*
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@ -5635,9 +5635,9 @@ has thrown a :ref:`C++ exception <exceptions>`.
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.. note::
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This function will always report "no error" when the LAMMPS library
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has been compiled without ``-DLAMMPS_EXCEPTIONS`` which turns fatal
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errors aborting LAMMPS into a C++ exceptions. You can use the library
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function :cpp:func:`lammps_config_has_exceptions` to check if this is
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has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
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errors aborting LAMMPS into C++ exceptions. You can use the library
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function :cpp:func:`lammps_config_has_exceptions` to check whether this is
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the case.
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\endverbatim
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*
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@ -5667,15 +5667,15 @@ error message is longer, it will be truncated accordingly. The return
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value of the function corresponds to the kind of error: a "1" indicates
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an error that occurred on all MPI ranks and is often recoverable, while
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a "2" indicates an abort that would happen only in a single MPI rank
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and thus may not be recoverable as other MPI ranks may be waiting on
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and thus may not be recoverable, as other MPI ranks may be waiting on
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the failing MPI ranks to send messages.
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.. note::
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This function will do nothing when the LAMMPS library has been
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compiled without ``-DLAMMPS_EXCEPTIONS`` which turns errors aborting
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LAMMPS into a C++ exceptions. You can use the library function
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:cpp:func:`lammps_config_has_exceptions` to check if this is the case.
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compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
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LAMMPS into C++ exceptions. You can use the library function
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:cpp:func:`lammps_config_has_exceptions` to check whether this is the case.
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\endverbatim
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*
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* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
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