ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Added reset_box, memory_usage, get_mpi_comm, extract_setting and associated documentation

Browse Source
This commit is contained in:
Karl Hammond
2022-08-10 00:55:17 -05:00
parent 7125682375
commit f442fc8540
2 changed files with 203 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
doc/src/Fortran.rst
View File

@ -187,6 +187,9 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
:f get_natoms: :f:func:`get_natoms`
:f get_thermo: :f:func:`get_thermo`
:f extract_box: :f:func:`extract_box`
:f reset_box: :f:func:`reset_box`
:f memory_usage: :f:func:`memory_usage`
:f extract_setting: :f:func:`extract_setting`
--------
@ -294,3 +297,54 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
:p logical boxflag [optional]: variable in which to store boolean denoting
whether the box will change during a simulation
(``.TRUE.`` means box will change)
--------
.. f:subroutine:: reset_box(boxlo, boxhi, xy, yz, xz)
:p real(c_double) boxlo [dimension(3)]: vector of three doubles containing
the lower box boundary
:p real(c_double) boxhi [dimension(3)]: vector of three doubles containing
the upper box boundary
:p real(c_double) xy: *x--y* tilt factor
:p real(c_double) yz: *y--z* tilt factor
:p real(c_double) xz: *x--z* tilt factor
--------
.. f:subroutine:: memory_usage(meminfo)
:p real(c_double) meminfo [dimension(3)]: vector of three doubles in which
to store memory usage data
--------
.. f:function:: get_mpi_comm()
:r integer: Fortran integer equivalent to the MPI communicator LAMMPS is
using
.. note::
The MPI_F08 module, which is in compliance with the Fortran 2008 standard,
is not directly supported by this function. However, you should be able to
convert between the two using the MPI_VAL member of the communicator. For
example,
.. code-block:: fortran
USE MPI_F08
USE LIBLAMMPS
TYPE (LAMMPS) :: lmp
TYPE (MPI_Comm) :: comm
! ... [commands to set up LAMMPS/etc.]
comm%MPI_VAL = lmp%get_mpi_comm()
should assign an MPI_F08 communicator properly.
--------
.. f:function:: extract_setting(keyword)
:p character(len=*) keyword: string containing the name of the thermo keyword
:r integer(c_int): value of the queried setting or :math:`-1` if unknown

159
fortran/lammps.f90
View File

@ -30,12 +30,44 @@
MODULE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_ptr, c_null_ptr, c_loc, &
c_int, c_char, c_null_char, c_double, c_size_t, c_f_pointer
c_int, c_int64_t, c_char, c_null_char, c_double, c_size_t, c_f_pointer
IMPLICIT NONE
PRIVATE
PUBLIC :: lammps
! These are public-interface constants that have the same purpose as the
! constants in library.h, except that their types match the type of the
! constant in question. Their purpose is to determine the type of the
! return value without something akin to a C/C++ type cast
INTEGER (c_int), PUBLIC, PARAMETER :: LMP_INT = 0_c_int
INTEGER (c_int), PUBLIC, DIMENSION(2), PARAMETER :: LMP_INT_1D = 1_c_int
INTEGER (c_int), PUBLIC, DIMENSION(2,2), PARAMETER :: LMP_INT_2D = 1_c_int
REAL (c_double), PUBLIC, PARAMETER :: LMP_DOUBLE = 2.0_c_double
REAL (c_double), PUBLIC, DIMENSION(2), PARAMETER :: &
LMP_DOUBLE_1D = 2.0_c_double
REAL (c_double), PUBLIC, DIMENSION(2,2), PARAMETER :: &
LMP_DOUBLE_2D = 3.0_c_double
INTEGER (c_int64_t), PUBLIC, PARAMETER :: LMP_INT64 = 4_c_int64_t
INTEGER (c_int64_t), PUBLIC, DIMENSION(2), PARAMETER :: &
LMP_INT64_1D = 4_c_int64_t
INTEGER (c_int64_t), PUBLIC, DIMENSION(2,2), PARAMETER :: &
LMP_INT64_2D = 5_c_int64_t
CHARACTER(LEN=*), PUBLIC, PARAMETER :: LMP_STRING = 'six'
! Data type constants for extracting data from global, atom, compute, and fix
!
! Must be kept in sync with the equivalent declarations in
! src/library.h and python/lammps/constants.py
INTEGER (c_int), PARAMETER :: &
LAMMPS_INT = 0_c_int, & ! 32-bit integer (array)
LAMMPS_INT_2D = 1, & ! two-dimensional 32-bit integer array
LAMMPS_DOUBLE = 2, & ! 64-bit double (array)
LAMMPS_DOUBLE_2D = 3, & ! two-dimensional 64-bit double array
LAMMPS_INT64 = 4, & ! 64-bit integer (array)
LAMMPS_INT64_2D = 5, & ! two-dimensional 64-bit integer array
LAMMPS_STRING = 6 ! C-String
TYPE lammps
TYPE(c_ptr) :: handle
CONTAINS
@ -44,10 +76,15 @@ MODULE LIBLAMMPS
PROCEDURE :: command => lmp_command
PROCEDURE :: commands_list => lmp_commands_list
PROCEDURE :: commands_string => lmp_commands_string
PROCEDURE :: version => lmp_version
PROCEDURE :: get_natoms => lmp_get_natoms
PROCEDURE :: get_thermo => lmp_get_thermo
PROCEDURE :: extract_box => lmp_extract_box
PROCEDURE :: reset_box => lmp_reset_box
PROCEDURE :: memory_usage => lmp_memory_usage
PROCEDURE :: get_mpi_comm => lmp_get_mpi_comm
PROCEDURE :: extract_setting => lmp_extract_setting
PROCEDURE :: version => lmp_version
END TYPE lammps
INTERFACE lammps
@ -117,7 +154,7 @@ MODULE LIBLAMMPS
END FUNCTION lammps_get_natoms
FUNCTION lammps_get_thermo(handle,name) BIND(C)
IMPORT :: c_ptr, c_double, c_char
IMPORT :: c_ptr, c_double
IMPLICIT NONE
REAL(c_double) :: lammps_get_thermo
TYPE(c_ptr), VALUE :: handle
@ -132,18 +169,47 @@ MODULE LIBLAMMPS
boxflag
END SUBROUTINE lammps_extract_box
! TODO
!SUBROUTINE lammps_reset_box
SUBROUTINE lammps_reset_box(handle,boxlo,boxhi,xy,yz,xz) BIND(C)
IMPORT :: c_ptr, c_double
IMPLICIT NONE
TYPE (c_ptr), VALUE :: handle
REAL (c_double), DIMENSION(3) :: boxlo, boxhi
REAL (c_double), VALUE :: xy, yz, xz
END SUBROUTINE lammps_reset_box
!SUBROUTINE lammps_memory_usage
SUBROUTINE lammps_memory_usage(handle,meminfo) BIND(C)
IMPORT :: c_ptr, c_double
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle
REAL(c_double), DIMENSION(*) :: meminfo
END SUBROUTINE lammps_memory_usage
!INTEGER (c_int) FUNCTION lammps_get_mpi_comm
!FIXME? type(MPI_Comm) FUNCTION lammps_get_mpi_comm
FUNCTION lammps_get_mpi_comm(handle) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE (c_ptr), VALUE :: handle
INTEGER (c_int) :: lammps_get_mpi_comm
END FUNCTION lammps_get_mpi_comm
!INTEGER (c_int) FUNCTION lammps_extract_setting
FUNCTION lammps_extract_setting(handle,keyword) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle, keyword
INTEGER (c_int) :: lammps_extract_setting
END FUNCTION lammps_extract_setting
!INTEGER (c_int) FUNCTION lammps_extract_global_datatype
FUNCTION lammps_extract_global_datatype(handle,name) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle, name
INTEGER (c_int) :: lammps_extract_global_datatype
END FUNCTION lammps_extract_global_datatype
FUNCTION lammps_extract_global(handle, name) BIND(C)
IMPORT :: c_ptr
TYPE(c_ptr), VALUE :: handle, name
TYPE(c_ptr) :: lammps_extract_global
END FUNCTION lammps_extract_global
!(generic) lammps_extract_global
! TODO: You can fake out the type-casting by declaring non-optional
! parameters that help the compiler figure out which one to call
@ -412,6 +478,79 @@ CONTAINS
IF ( PRESENT(boxflag) ) boxflag = ( C_boxflag /= 0_C_int )
END SUBROUTINE lmp_extract_box
! equivalent function to lammps_reset_box
SUBROUTINE lmp_reset_box (self, boxlo, boxhi, xy, yz, xz)
CLASS(lammps), INTENT(IN) :: self
REAL(C_double), INTENT(IN) :: boxlo(3), boxhi(3), xy, yz, xz
CALL lammps_reset_box (self%handle, boxlo, boxhi, xy, yz, xz)
END SUBROUTINE lmp_reset_box
! equivalent function to lammps_memory_usage
SUBROUTINE lmp_memory_usage(self,meminfo)
CLASS(lammps), INTENT(IN) :: self
INTEGER, PARAMETER :: MEMINFO_ELEM = 3
REAL (c_double), DIMENSION(MEMINFO_ELEM), INTENT(OUT) :: meminfo
CALL lammps_memory_usage(self%handle,meminfo)
END SUBROUTINE lmp_memory_usage
! equivalent function to lammps_get_mpi_comm
INTEGER FUNCTION lmp_get_mpi_comm (self)
CLASS(lammps), INTENT(IN) :: self
lmp_get_mpi_comm = lammps_get_mpi_comm(self%handle)
END FUNCTION lmp_get_mpi_comm
! equivalent function to lammps_extract_setting
INTEGER (c_int) FUNCTION lmp_extract_setting (self, keyword)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: keyword
TYPE(c_ptr) :: Ckeyword
Ckeyword = f2c_string(keyword)
lmp_extract_setting = lammps_extract_setting(self%handle, Ckeyword)
CALL lammps_free(Ckeyword)
END FUNCTION lmp_extract_setting
! equivalent function to lammps_extract_global_datatype
! this function doesn't need to be accessed by the user, but is instead used
! for type checking
INTEGER (c_int) FUNCTION lmp_extract_global_datatype (self, name)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: name
TYPE(c_ptr) :: Cname
Cname = f2c_string(name)
lmp_extract_global_datatype &
= lammps_extract_global_datatype(self%handle, Cname)
CALL lammps_free(Cname)
END FUNCTION lmp_extract_global_datatype
! equivalent functions to lammps_extract_global (overloaded)
FUNCTION lmp_extract_global_int (self, name, dtype)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: name
INTEGER(c_int) :: dtype
INTEGER(c_int) :: lmp_extract_global_int
TYPE(c_ptr) :: Cname, Cptr
INTEGER(c_int) :: datatype
INTEGER(c_int), POINTER :: ptr
Cname = f2c_string(name)
datatype = lammps_extract_global_datatype(self%handle, Cname)
IF ( datatype /= LAMMPS_INT ) THEN
! throw an exception or something; data type doesn't match!
END IF
Cptr = lammps_extract_global(self%handle, Cname)
CALL c_f_pointer(Cptr, ptr)
lmp_extract_global_int = ptr
CALL lammps_free(Cname)
END FUNCTION lmp_extract_global_int
! TODO need more generics here to match TKR of LMP_INT_1D, LMP_BIGINT,
! LMP_DOUBLE, LMP_DOUBLE_1D, LMS_STRING [this assumes no one adds anything
! requiring LMP_DOUBLE_2D and the like!]
! equivalent function to lammps_version()
INTEGER FUNCTION lmp_version(self)
IMPLICIT NONE