Fixed spacing
This commit is contained in:
Karl Hammond
@ -363,8 +363,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
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If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For
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more details please see the documentation of :cpp:func:`lammps_open`.
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:o character(len=\*) args(\*) [optional]: arguments as list of strings
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:o integer comm [optional]: MPI communicator
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:o args: arguments as list of strings
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:otype args: character(len=\*),dimension(:),optional
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:o comm: MPI communicator
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:otype comm: integer,optional
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:to: :cpp:func:`lammps_open_fortran`
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:to: :cpp:func:`lammps_open_no_mpi`
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:r lammps: an instance of the :f:type:`lammps` derived type
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@ -415,8 +417,9 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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has a value of ``.TRUE.``, then this subroutine also calls
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:cpp:func:`lammps_mpi_finalize`.
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:o logical finalize [optional]: shut down the MPI environment of the LAMMPS
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:o finalize: shut down the MPI environment of the LAMMPS
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library if ``.TRUE.``.
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:otype finalize: logical,optional
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:to: :cpp:func:`lammps_close`
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--------
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@ -428,7 +431,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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.. versionadded:: TBD
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:p integer error_type: constant to select which Error class function to call
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:p error_type: constant to select which Error class function to call
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:ptype error_type: integer
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:p character(len=\*) error_text: error message
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:to: :cpp:func:`lammps_error`
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@ -520,11 +524,13 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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:o real(c_double) xy [optional]: variable in which to store *xy* tilt factor
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:o real(c_double) yz [optional]: variable in which to store *yz* tilt factor
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:o real(c_double) xz [optional]: variable in which to store *xz* tilt factor
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:o logical pflags [dimension(3),optional]: vector in which to store
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:o pflags: vector in which to store
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periodicity flags (``.TRUE.`` means periodic in that dimension)
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:o logical boxflag [optional]: variable in which to store boolean denoting
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:otype pflags: logical,dimension(3),optional
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:o boxflag: variable in which to store boolean denoting
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whether the box will change during a simulation
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(``.TRUE.`` means box will change)
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:otype boxflag: logical,optional
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:to: :cpp:func:`lammps_extract_box`
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.. note::
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@ -829,7 +835,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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x0(0:,0:) => x
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The above would cause the dimensions of *x* to be (1:3, 1:nmax)
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and those of *x0* to be (0:2, 0:nmax-1).
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and those of *x0* to be (0:2, 0:nmax\ :math:`-`\ 1).
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--------
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@ -1338,12 +1344,13 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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*data* must be of length (*count* :math:`\times` *natoms*).
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:p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*)
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:p polymorphic data [dimension(:)]: per-atom values packed in a one-dimensional array
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:p data: per-atom values packed in a one-dimensional array
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containing the data to be scattered. This array must have length *natoms*
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(e.g., for *type* or *charge*) or length *natoms*\ :math:`\times 3`
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(e.g., for *x* or *f*). The array *data* must be rank 1 (i.e.,
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``DIMENSION(:)``) and be of type ``INTEGER(c_int)`` (e.g., for *mask* or
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*type*) or of type ``REAL(c_double)`` (e.g., for *x* or *charge* or *f*).
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:ptype data: polymorphic,dimension(:)
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:to: :cpp:func:`lammps_scatter_atoms`
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--------
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@ -1370,12 +1377,13 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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:p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*)
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:p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms
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being scattered
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:p polymorphic data [dimension(:)]: per-atom values packed into a
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:p data: per-atom values packed into a
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one-dimensional array containing the data to be scattered. This array must
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have either the same length as *ids* (for *mask*, *type*, etc.) or three
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times its length (for *x*, *f*, etc.); the array must be rank 1
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and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type
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``REAL(c_double)`` (e.g., for *charge*, *x*, or *f*).
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:ptype data: polymorphic,dimension(:)
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:to: :cpp:func:`lammps_scatter_atoms_subset`
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--------
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@ -1393,20 +1401,21 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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:p real(c_double) x [dimension(3N)]: vector of :math:`3N` x/y/z positions
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of the new atoms, arranged as :math:`[x_1,y_1,z_1,x_2,y_2,\dotsc]`
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(required/see note below)
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:o integer(\*) id [dimension(N)]: vector of :math:`N` atom IDs; if
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absent, LAMMPS will generate them for you. \*The kind parameter should be
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``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which
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:o integer(kind=\*) id [dimension(N)]: vector of :math:`N` atom IDs; if
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absent, LAMMPS will generate them for you. \*The ``KIND`` parameter should
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be ``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which
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case it should be ``c_int64_t``.
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:o real(c_double) v [dimension(3N)]: vector of :math:`3N` x/y/z velocities
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of the new atoms, arranged as :math:`[v_{1,x},v_{1,y},v_{1,z},v_{2,x},
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\dotsc]`; if absent, they will be set to zero
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:o integer(\*) image [dimension(N)]: vector of :math:`N` image flags; if
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absent, they are set to zero. \*The kind parameter should be
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:o integer(kind=\*) image [dimension(N)]: vector of :math:`N` image flags;
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if absent, they are set to zero. \*The ``KIND`` parameter should be
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``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which
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case it should be ``c_int64_t``. See note below.
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:o logical bexpand: if ``.TRUE.``, atoms outside of shrink-wrap boundaries
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:o bexpand: if ``.TRUE.``, atoms outside of shrink-wrap boundaries
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will be created, not dropped, and the box dimensions will be extended.
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Default is ``.FALSE.``
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:otype bexpand: logical
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:to: :cpp:func:`lammps_create_atoms`
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.. note::
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@ -1639,8 +1648,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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:p character(len=:) package [dimension(:),allocatable]: list of packages;
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*must* have the ``ALLOCATABLE`` attribute and be of rank 1
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(i.e., ``DIMENSION(:)``) with allocatable length.
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:o integer length [optional]: length of each string in the list.
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Default: 31.
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:o length: length of each string in the list. Default: 31.
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:otype length: integer,optional
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:to: :cpp:func:`lammps_config_package_count`
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:to: :cpp:func:`lammps_config_package_name`
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@ -1796,7 +1805,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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.. note::
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The fact that the programmer does not know the kind parameter of the
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The fact that the programmer does not know the ``KIND`` parameter of the
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return value until compile time means that it is impossible to define an
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interface that works for both sizes of ``imageint``. One side effect of
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this is that you must assign the return value of this function to a
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@ -1855,7 +1864,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
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applications to determine if the LAMMPS instance is currently active.
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:to: :cpp:func:`lammps_is_running`
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:r logical: ``.FALSE.`` if idle or ``.TRUE.`` if active
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:r is_running: ``.FALSE.`` if idle or ``.TRUE.`` if active
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:rtype is_running: logical
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--------
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