forked from lijiext/lammps
983 lines
40 KiB
Fortran
983 lines
40 KiB
Fortran
!! -----------------------------------------------------------------------
|
|
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
! www.cs.sandia.gov/~sjplimp/lammps.html
|
|
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
|
!
|
|
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
! certain rights in this software. This software is distributed under
|
|
! the GNU General Public License.
|
|
!
|
|
! See the README file in the top-level LAMMPS directory.
|
|
!--------------------------------------------------------------------------
|
|
|
|
!! ------------------------------------------------------------------------
|
|
! Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
|
|
! University of Tennessee, Knoxville (USA), 2012
|
|
!--------------------------------------------------------------------------
|
|
|
|
!! LAMMPS, a Fortran 2003 module containing an interface between Fortran
|
|
!! programs and the C-style functions in library.cpp that ship with LAMMPS.
|
|
!! This file should be accompanied by LAMMPS-wrapper.cpp and LAMMPS-wrapper.h,
|
|
!! which define wrapper functions that ease portability and enforce array
|
|
!! dimensions.
|
|
!!
|
|
!! Everything in this module should be 100% portable by way of Fortran 2003's
|
|
!! ISO_C_BINDING intrinsic module. See the README for instructions for
|
|
!! compilation and use.
|
|
!!
|
|
!! Here are the PUBLIC functions and subroutines included in this module.
|
|
!! subroutine lammps_open (command_line, communicator, ptr)
|
|
!! subroutine lammps_open_no_mpi (command_line, ptr)
|
|
!! subroutine lammps_close (ptr)
|
|
!! subroutine lammps_file (ptr, str)
|
|
!! subroutine lammps_command (ptr, str)
|
|
!! subroutine lammps_free (ptr)
|
|
!! subroutine lammps_extract_global (global, ptr, name)
|
|
!! subroutine lammps_extract_atom (atom, ptr, name)
|
|
!! subroutine lammps_extract_fix (fix, ptr, id, style, type, i, j)
|
|
!! subroutine lammps_extract_compute (compute, ptr, id, style, type)
|
|
!! subroutine lammps_extract_variable (variable, ptr, name, group)
|
|
!! function lammps_get_natoms (ptr)
|
|
!! subroutine lammps_gather_atoms (ptr, name, count, data)
|
|
!! subroutine lammps_scatter_atoms (ptr, name, data)
|
|
|
|
#define FLERR __FILE__,__LINE__
|
|
! The above line allows for similar error checking as is done with standard
|
|
! LAMMPS files.
|
|
|
|
module LAMMPS
|
|
|
|
use, intrinsic :: ISO_C_binding, only : C_double, C_int, C_ptr, C_char, &
|
|
C_NULL_CHAR, C_loc, C_F_pointer, lammps_instance => C_ptr
|
|
implicit none
|
|
private
|
|
public :: lammps_set_user_virial
|
|
public :: lammps_set_external_vector_length
|
|
public :: lammps_set_external_vector
|
|
public :: lammps_set_user_energy
|
|
public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, &
|
|
lammps_command, lammps_free, lammps_extract_global, &
|
|
lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, &
|
|
lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, &
|
|
lammps_set_callback
|
|
public :: lammps_scatter_atoms, lammps_instance, C_ptr, C_double, C_int
|
|
|
|
!! Functions supplemental to the prototypes in library.h. {{{1
|
|
!! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
|
|
!! I would have written the first in Fortran, but the MPI libraries (which
|
|
!! were written in C) have C-based functions to convert from Fortran MPI
|
|
!! handles to C MPI handles, and there is no Fortran equivalent for those
|
|
!! functions.
|
|
interface
|
|
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
|
|
bind (C, name='lammps_open_fortran_wrapper')
|
|
import :: C_int, C_ptr
|
|
integer (C_int), value :: argc
|
|
type (C_ptr), dimension(*) :: argv
|
|
integer, value :: communicator
|
|
type (C_ptr) :: ptr
|
|
end subroutine lammps_open_wrapper
|
|
subroutine lammps_actual_error_all (ptr, file, line, str) &
|
|
bind (C, name='lammps_error_all')
|
|
import :: C_int, C_char, C_ptr
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*), intent(in) :: file, str
|
|
integer (C_int), value :: line
|
|
end subroutine lammps_actual_error_all
|
|
function lammps_get_ntypes (ptr) result (ntypes) &
|
|
bind (C, name='lammps_get_ntypes')
|
|
import :: C_int, C_ptr
|
|
type (C_ptr), value :: ptr
|
|
integer (C_int) :: ntypes
|
|
end function lammps_get_ntypes
|
|
function lammps_actual_extract_compute_vectorsize (ptr, id, style) &
|
|
result (vectorsize) bind (C, name='lammps_extract_compute_vectorsize')
|
|
import :: C_int, C_char, C_ptr
|
|
integer (C_int) :: vectorsize
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: id
|
|
integer (C_int), value :: style
|
|
end function lammps_actual_extract_compute_vectorsize
|
|
subroutine lammps_actual_extract_compute_arraysize (ptr, id, style, &
|
|
nrows, ncols) bind (C, name='lammps_extract_compute_arraysize')
|
|
import :: C_int, C_char, C_ptr
|
|
integer (C_int) :: arraysize
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: id
|
|
integer (C_int), value :: style
|
|
integer (C_int) :: nrows, ncols
|
|
end subroutine lammps_actual_extract_compute_arraysize
|
|
function lammps_actual_extract_fix_vectorsize (ptr, id, style) &
|
|
result (vectorsize) bind (C, name='lammps_extract_fix_vectorsize')
|
|
import :: C_int, C_char, C_ptr
|
|
integer (C_int) :: vectorsize
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: id
|
|
integer (C_int), value :: style
|
|
end function lammps_actual_extract_fix_vectorsize
|
|
subroutine lammps_actual_extract_fix_arraysize (ptr, id, style, &
|
|
nrows, ncols) bind (C, name='lammps_extract_fix_arraysize')
|
|
import :: C_int, C_char, C_ptr
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: id
|
|
integer (C_int), value :: style
|
|
integer (C_int) :: nrows, ncols
|
|
end subroutine lammps_actual_extract_fix_arraysize
|
|
end interface
|
|
|
|
!! Functions/subroutines defined in library.h and library.cpp {{{1
|
|
interface
|
|
subroutine lammps_actual_open_no_mpi (argc, argv, ptr) &
|
|
bind (C, name='lammps_open_no_mpi')
|
|
import :: C_int, C_ptr
|
|
integer (C_int), value :: argc
|
|
type (C_ptr), dimension(*) :: argv
|
|
type (C_ptr) :: ptr
|
|
end subroutine lammps_actual_open_no_mpi
|
|
|
|
subroutine lammps_close (ptr) bind (C, name='lammps_close')
|
|
import :: C_ptr
|
|
type (C_ptr), value :: ptr
|
|
end subroutine lammps_close
|
|
|
|
subroutine lammps_actual_file (ptr, str) bind (C, name='lammps_file')
|
|
import :: C_ptr, C_char
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: str
|
|
end subroutine lammps_actual_file
|
|
|
|
function lammps_actual_command (ptr, str) result (command) &
|
|
bind (C, name='lammps_command')
|
|
import :: C_ptr, C_char
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: str
|
|
type (C_ptr) :: command
|
|
end function lammps_actual_command
|
|
|
|
subroutine lammps_free (ptr) bind (C, name='lammps_free')
|
|
import :: C_ptr
|
|
type (C_ptr), value :: ptr
|
|
end subroutine lammps_free
|
|
|
|
function lammps_actual_extract_global (ptr, name) &
|
|
bind (C, name='lammps_extract_global') result (global)
|
|
import :: C_ptr, C_char
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: name
|
|
type (C_ptr) :: global
|
|
end function lammps_actual_extract_global
|
|
|
|
function lammps_actual_extract_atom (ptr, name) &
|
|
bind (C, name='lammps_extract_atom') result (atom)
|
|
import :: C_ptr, C_char
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: name
|
|
type (C_ptr) :: atom
|
|
end function lammps_actual_extract_atom
|
|
|
|
function lammps_actual_extract_compute (ptr, id, style, type) &
|
|
result (compute) bind (C, name='lammps_extract_compute')
|
|
import :: C_ptr, C_char, C_int
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: id
|
|
integer (C_int), value :: style, type
|
|
type (C_ptr) :: compute
|
|
end function lammps_actual_extract_compute
|
|
|
|
function lammps_actual_extract_fix (ptr, id, style, type, i, j) &
|
|
result (fix) bind (C, name='lammps_extract_fix')
|
|
import :: C_ptr, C_char, C_int
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: id
|
|
integer (C_int), value :: style, type, i, j
|
|
type (C_ptr) :: fix
|
|
end function lammps_actual_extract_fix
|
|
|
|
function lammps_actual_extract_variable (ptr, name, group) &
|
|
result (variable) bind (C, name='lammps_extract_variable')
|
|
import :: C_ptr, C_char
|
|
type (C_ptr), value :: ptr
|
|
character (kind=C_char), dimension(*) :: name, group
|
|
type (C_ptr) :: variable
|
|
end function lammps_actual_extract_variable
|
|
|
|
function lammps_get_natoms (ptr) result (natoms) &
|
|
bind (C, name='lammps_get_natoms')
|
|
import :: C_ptr, C_int
|
|
type (C_ptr), value :: ptr
|
|
integer (C_int) :: natoms
|
|
end function lammps_get_natoms
|
|
|
|
subroutine lammps_set_callback (ptr) &
|
|
bind (C, name='lammps_set_callback')
|
|
import :: C_ptr
|
|
type (C_ptr), value :: ptr
|
|
end subroutine lammps_set_callback
|
|
|
|
subroutine lammps_set_user_energy (ptr, energy) &
|
|
bind (C, name='lammps_set_user_energy')
|
|
import :: C_ptr, C_double
|
|
type (C_ptr), value :: ptr
|
|
real(C_double), value :: energy
|
|
end subroutine lammps_set_user_energy
|
|
|
|
subroutine lammps_set_user_virial (ptr, virial) &
|
|
bind (C, name='lammps_set_user_virial')
|
|
import :: C_ptr, C_double
|
|
type (C_ptr), value :: ptr
|
|
real(C_double) :: virial(6)
|
|
end subroutine lammps_set_user_virial
|
|
|
|
subroutine lammps_set_external_vector_length (ptr, n) &
|
|
bind (C, name='lammps_set_external_vector_length')
|
|
import :: C_ptr, C_double, C_int
|
|
type(C_ptr), value :: ptr
|
|
integer (C_int), value :: n
|
|
end subroutine lammps_set_external_vector_length
|
|
|
|
subroutine lammps_set_external_vector (ptr, n, val) &
|
|
bind (C, name='lammps_set_external_vector')
|
|
import :: C_ptr, C_int, C_double
|
|
type (C_ptr), value :: ptr
|
|
integer (C_int), value :: n
|
|
real(C_double), value :: val
|
|
end subroutine lammps_set_external_vector
|
|
|
|
subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
|
|
bind (C, name='lammps_gather_atoms')
|
|
import :: C_ptr, C_int, C_char
|
|
type (C_ptr), value :: ptr, data
|
|
character (kind=C_char), dimension(*) :: name
|
|
integer (C_int), value :: type, count
|
|
end subroutine lammps_actual_gather_atoms
|
|
|
|
subroutine lammps_actual_scatter_atoms (ptr, name, type, count, data) &
|
|
bind (C, name='lammps_scatter_atoms')
|
|
import :: C_ptr, C_int, C_char
|
|
type (C_ptr), value :: ptr, data
|
|
character (kind=C_char), dimension(*) :: name
|
|
integer (C_int), value :: type, count
|
|
end subroutine lammps_actual_scatter_atoms
|
|
end interface
|
|
|
|
! Generic functions for the wrappers below {{{1
|
|
|
|
interface lammps_extract_global
|
|
module procedure lammps_extract_global_i, &
|
|
lammps_extract_global_dp
|
|
end interface lammps_extract_global
|
|
|
|
interface lammps_extract_atom
|
|
module procedure lammps_extract_atom_ia, &
|
|
lammps_extract_atom_dpa, &
|
|
lammps_extract_atom_dp2a
|
|
end interface lammps_extract_atom
|
|
|
|
interface lammps_extract_compute
|
|
module procedure lammps_extract_compute_dp, &
|
|
lammps_extract_compute_dpa, &
|
|
lammps_extract_compute_dp2a
|
|
end interface lammps_extract_compute
|
|
|
|
interface lammps_extract_fix
|
|
module procedure lammps_extract_fix_dp, &
|
|
lammps_extract_fix_dpa, &
|
|
lammps_extract_fix_dp2a
|
|
end interface lammps_extract_fix
|
|
|
|
interface lammps_extract_variable
|
|
module procedure lammps_extract_variable_dp, &
|
|
lammps_extract_variable_dpa
|
|
end interface lammps_extract_variable
|
|
|
|
interface lammps_gather_atoms
|
|
module procedure lammps_gather_atoms_ia, lammps_gather_atoms_dpa
|
|
end interface lammps_gather_atoms
|
|
|
|
interface lammps_scatter_atoms
|
|
module procedure lammps_scatter_atoms_ia, lammps_scatter_atoms_dpa
|
|
end interface lammps_scatter_atoms
|
|
|
|
contains !! Wrapper functions local to this module {{{1
|
|
|
|
subroutine lammps_open (command_line, communicator, ptr)
|
|
character (len=*), intent(in) :: command_line
|
|
integer, intent(in) :: communicator
|
|
type (C_ptr) :: ptr
|
|
integer (C_int) :: argc
|
|
type (C_ptr), dimension(:), allocatable :: argv
|
|
character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
|
|
c_command_line
|
|
c_command_line = string2Cstring (command_line)
|
|
call Cstring2argcargv (c_command_line, argc, argv)
|
|
call lammps_open_wrapper (argc, argv, communicator, ptr)
|
|
deallocate (argv)
|
|
end subroutine lammps_open
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine lammps_open_no_mpi (command_line, ptr)
|
|
character (len=*), intent(in) :: command_line
|
|
type (C_ptr) :: ptr
|
|
integer (C_int) :: argc
|
|
type (C_ptr), dimension(:), allocatable :: argv
|
|
character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
|
|
c_command_line
|
|
c_command_line = string2Cstring (command_line)
|
|
call Cstring2argcargv (c_command_line, argc, argv)
|
|
call lammps_actual_open_no_mpi (argc, argv, ptr)
|
|
deallocate (argv)
|
|
end subroutine lammps_open_no_mpi
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine lammps_file (ptr, str)
|
|
type (C_ptr) :: ptr
|
|
character (len=*) :: str
|
|
character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
|
|
Cstr = string2Cstring (str)
|
|
call lammps_actual_file (ptr, Cstr)
|
|
end subroutine lammps_file
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine lammps_command (ptr, str)
|
|
type (C_ptr) :: ptr
|
|
character (len=*) :: str
|
|
character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
|
|
type (C_ptr) :: dummy
|
|
Cstr = string2Cstring (str)
|
|
dummy = lammps_actual_command (ptr, Cstr)
|
|
end subroutine lammps_command
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
! lammps_extract_global {{{2
|
|
function lammps_extract_global_Cptr (ptr, name) result (global)
|
|
type (C_ptr) :: global
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
|
|
Cname = string2Cstring (name)
|
|
global = lammps_actual_extract_global (ptr, Cname)
|
|
end function lammps_extract_global_Cptr
|
|
subroutine lammps_extract_global_i (global, ptr, name)
|
|
integer (C_int), pointer, intent(out) :: global
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
type (C_ptr) :: Cptr
|
|
Cptr = lammps_extract_global_Cptr (ptr, name)
|
|
call C_F_pointer (Cptr, global)
|
|
end subroutine lammps_extract_global_i
|
|
subroutine lammps_extract_global_dp (global, ptr, name)
|
|
real (C_double), pointer, intent(out) :: global
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
type (C_ptr) :: Cptr
|
|
Cptr = lammps_extract_global_Cptr (ptr, name)
|
|
call C_F_pointer (Cptr, global)
|
|
end subroutine lammps_extract_global_dp
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
! lammps_extract_atom {{{2
|
|
function lammps_extract_atom_Cptr (ptr, name) result (atom)
|
|
type (C_ptr) :: atom
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
|
|
Cname = string2Cstring (name)
|
|
atom = lammps_actual_extract_atom (ptr, Cname)
|
|
end function lammps_extract_atom_Cptr
|
|
subroutine lammps_extract_atom_ia (atom, ptr, name)
|
|
integer (C_int), dimension(:), pointer, intent(out) :: atom
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
type (C_ptr) :: Cptr
|
|
integer (C_int), pointer :: nelements
|
|
call lammps_extract_global_i (nelements, ptr, 'nlocal')
|
|
Cptr = lammps_extract_atom_Cptr (ptr, name)
|
|
call C_F_pointer (Cptr, atom, (/nelements/))
|
|
end subroutine lammps_extract_atom_ia
|
|
subroutine lammps_extract_atom_dpa (atom, ptr, name)
|
|
real (C_double), dimension(:), pointer, intent(out) :: atom
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
type (C_ptr) :: Cptr
|
|
integer (C_int), pointer :: nlocal
|
|
integer :: nelements
|
|
real (C_double), dimension(:), pointer :: Fptr
|
|
if ( name == 'mass' ) then
|
|
nelements = lammps_get_ntypes (ptr) + 1
|
|
else if ( name == 'x' .or. name == 'v' .or. name == 'f' .or. &
|
|
name == 'mu' .or. name == 'omega' .or. name == 'torque' .or. &
|
|
name == 'angmom' ) then
|
|
! We should not be getting a rank-2 array here!
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
|
|
& data (' // trim(name) // ') into a rank 1 array.')
|
|
return
|
|
else
|
|
! Everything else we can get is probably nlocal units long
|
|
call lammps_extract_global_i (nlocal, ptr, 'nlocal')
|
|
nelements = nlocal
|
|
end if
|
|
Cptr = lammps_extract_atom_Cptr (ptr, name)
|
|
call C_F_pointer (Cptr, Fptr, (/nelements/))
|
|
if ( name == 'mass' ) then
|
|
!atom(0:) => Fptr
|
|
atom => Fptr
|
|
else
|
|
atom => Fptr
|
|
end if
|
|
end subroutine lammps_extract_atom_dpa
|
|
subroutine lammps_extract_atom_dp2a (atom, ptr, name)
|
|
real (C_double), dimension(:,:), pointer, intent(out) :: atom
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
type (C_ptr) :: Cptr
|
|
type (C_ptr), pointer, dimension(:) :: Catom
|
|
integer (C_int), pointer :: nelements
|
|
if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' .and. &
|
|
name /= 'mu' .and. name /= 'omega' .and. name /= 'tandque' .and. &
|
|
name /= 'angmom' .and. name /= 'fexternal' ) then
|
|
! We should not be getting a rank-2 array here!
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
|
|
& data (' // trim(name) // ') into a rank 2 array.')
|
|
return
|
|
end if
|
|
Cptr = lammps_extract_atom_Cptr (ptr, name)
|
|
call lammps_extract_global_i (nelements, ptr, 'nlocal')
|
|
! Catom will now be the array of void* pointers that the void** pointer
|
|
! pointed to. Catom(1) is now the pointer to the first element.
|
|
call C_F_pointer (Cptr, Catom, (/nelements/))
|
|
! Now get the actual array, which has its shape transposed from what we
|
|
! might think of it in C
|
|
call C_F_pointer (Catom(1), atom, (/3, nelements/))
|
|
end subroutine lammps_extract_atom_dp2a
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
! lammps_extract_compute {{{2
|
|
function lammps_extract_compute_Cptr (ptr, id, style, type) result (compute)
|
|
type (C_ptr) :: compute
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type
|
|
integer (kind=C_int) :: Cstyle, Ctype
|
|
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
|
|
Cid = string2Cstring (id)
|
|
Cstyle = style
|
|
Ctype = type
|
|
compute = lammps_actual_extract_compute (ptr, Cid, Cstyle, Ctype)
|
|
end function lammps_extract_compute_Cptr
|
|
subroutine lammps_extract_compute_dp (compute, ptr, id, style, type)
|
|
real (C_double), pointer, intent(out) :: compute
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type
|
|
type (C_ptr) :: Cptr
|
|
! The only valid values of (style,type) are (0,0) for scalar 'compute'
|
|
if ( style /= 0 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot pack per-atom/local&
|
|
& data into a scalar.')
|
|
return
|
|
end if
|
|
if ( type == 1 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
|
|
& vector (rank 1) into a scalar.')
|
|
return
|
|
else if ( type == 2 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
|
|
& array (rank 2) into a scalar.')
|
|
return
|
|
end if
|
|
Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
|
|
call C_F_pointer (Cptr, compute)
|
|
end subroutine lammps_extract_compute_dp
|
|
subroutine lammps_extract_compute_dpa (compute, ptr, id, style, type)
|
|
real (C_double), dimension(:), pointer, intent(out) :: compute
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type
|
|
type (C_ptr) :: Cptr
|
|
integer :: nelements
|
|
! Check for the correct dimensionality
|
|
if ( type == 0 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
|
|
& scalar (rank 0) into a rank 1 variable.')
|
|
return
|
|
else if ( type == 2 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
|
|
& array (rank 2) into a rank 1 variable.')
|
|
return
|
|
end if
|
|
nelements = lammps_extract_compute_vectorsize (ptr, id, style)
|
|
Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
|
|
call C_F_pointer (Cptr, compute, (/nelements/))
|
|
end subroutine lammps_extract_compute_dpa
|
|
subroutine lammps_extract_compute_dp2a (compute, ptr, id, style, type)
|
|
real (C_double), dimension(:,:), pointer, intent(out) :: compute
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type
|
|
type (C_ptr) :: Cptr
|
|
type (C_ptr), pointer, dimension(:) :: Ccompute
|
|
integer :: nr, nc
|
|
! Check for the correct dimensionality
|
|
if ( type == 0 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
|
|
& scalar (rank 0) into a rank 2 variable.')
|
|
return
|
|
else if ( type == 1 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
|
|
& array (rank 1) into a rank 2 variable.')
|
|
return
|
|
end if
|
|
call lammps_extract_compute_arraysize (ptr, id, style, nr, nc)
|
|
Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
|
|
call C_F_pointer (Cptr, Ccompute, (/nr/))
|
|
! Note that the matrix is transposed, from Fortran's perspective
|
|
call C_F_pointer (Ccompute(1), compute, (/nc, nr/))
|
|
end subroutine lammps_extract_compute_dp2a
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
! lammps_extract_fix {{{2
|
|
function lammps_extract_fix_Cptr (ptr, id, style, type, i, j) &
|
|
result (fix)
|
|
type (C_ptr) :: fix
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type, i, j
|
|
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
|
|
integer (kind=C_int) :: Cstyle, Ctype, Ci, Cj
|
|
Cid = string2Cstring (id)
|
|
Cstyle = style
|
|
Ctype = type
|
|
Ci = i - 1 ! This is for consistency with the values from f_ID[i],
|
|
Cj = j - 1 ! which is different from what library.cpp uses!
|
|
if ( (type >= 1 .and. Ci < 0) .or. &
|
|
(type == 2 .and. (Ci < 0 .or. Cj < 0) ) ) then
|
|
call lammps_error_all (ptr, FLERR, 'Index out of range in&
|
|
& lammps_extract_fix')
|
|
end if
|
|
fix = lammps_actual_extract_fix (ptr, Cid, Cstyle, Ctype, Ci, Cj)
|
|
end function lammps_extract_fix_Cptr
|
|
subroutine lammps_extract_fix_dp (fix, ptr, id, style, type, i, j)
|
|
real (C_double), intent(out) :: fix
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type, i, j
|
|
type (C_ptr) :: Cptr
|
|
real (C_double), pointer :: Fptr
|
|
! Check for the correct dimensionality
|
|
if ( style /= 0 ) then
|
|
select case (type)
|
|
case (0)
|
|
call lammps_error_all (ptr, FLERR, 'There is no per-atom or local&
|
|
& scalar data available from fixes.')
|
|
case (1)
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
|
|
&per-atom/local vector (rank 1) into a scalar.')
|
|
case (2)
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
|
|
&per-atom/local array (rank 2) into a scalar.')
|
|
case default
|
|
call lammps_error_all (ptr, FLERR, 'Invalid extract_fix style/&
|
|
&type combination.')
|
|
end select
|
|
return
|
|
end if
|
|
Cptr = lammps_extract_fix_Cptr (ptr, id, style, type, i, j)
|
|
call C_F_pointer (Cptr, Fptr)
|
|
fix = Fptr
|
|
nullify (Fptr)
|
|
! Memory is only allocated for "global" fix variables
|
|
if ( style == 0 ) call lammps_free (Cptr)
|
|
end subroutine lammps_extract_fix_dp
|
|
subroutine lammps_extract_fix_dpa (fix, ptr, id, style, type, i, j)
|
|
real (C_double), dimension(:), pointer, intent(out) :: fix
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type, i, j
|
|
type (C_ptr) :: Cptr
|
|
integer :: fix_len
|
|
! Check for the correct dimensionality
|
|
if ( style == 0 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You can''t extract the&
|
|
& whole vector from global fix data')
|
|
return
|
|
else if ( type == 0 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You can''t extract a fix&
|
|
& scalar into a rank 1 variable')
|
|
return
|
|
else if ( type == 2 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
|
|
& array into a rank 1 variable.')
|
|
return
|
|
else if ( type /= 1 ) then
|
|
call lammps_error_all (ptr, FLERR, 'Invalid type for fix extraction.')
|
|
return
|
|
end if
|
|
fix_len = lammps_extract_fix_vectorsize (ptr, id, style)
|
|
call C_F_pointer (Cptr, fix, (/fix_len/))
|
|
! Memory is only allocated for "global" fix variables, which we should
|
|
! never get here, so no need to call lammps_free!
|
|
end subroutine lammps_extract_fix_dpa
|
|
subroutine lammps_extract_fix_dp2a (fix, ptr, id, style, type, i, j)
|
|
real (C_double), dimension(:,:), pointer, intent(out) :: fix
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style, type, i, j
|
|
type (C_ptr) :: Cptr
|
|
type (C_ptr), pointer, dimension(:) :: Cfix
|
|
integer :: nr, nc
|
|
! Check for the correct dimensionality
|
|
if ( style == 0 ) then
|
|
call lammps_error_all (ptr, FLERR, 'It is not possible to extract the&
|
|
& entire array from global fix data.')
|
|
return
|
|
else if ( type == 0 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
|
|
& scalar (rank 0) into a rank 2 variable.')
|
|
return
|
|
else if ( type == 1 ) then
|
|
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
|
|
& vector (rank 1) into a rank 2 variable.')
|
|
return
|
|
end if
|
|
call lammps_extract_fix_arraysize (ptr, id, style, nr, nc)
|
|
! Extract pointer to first element as Cfix(1)
|
|
call C_F_pointer (Cptr, Cfix, (/nr/))
|
|
! Now extract the array, which is transposed
|
|
call C_F_pointer (Cfix(1), fix, (/nc, nr/))
|
|
end subroutine lammps_extract_fix_dp2a
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
! lammps_extract_variable {{{2
|
|
function lammps_extract_variable_Cptr (ptr, name, group) result (variable)
|
|
type (C_ptr) :: ptr, variable
|
|
character (len=*) :: name
|
|
character (len=*), optional :: group
|
|
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
|
|
character (kind=C_char), dimension(:), allocatable :: Cgroup
|
|
Cname = string2Cstring (name)
|
|
if ( present(group) ) then
|
|
allocate (Cgroup(len_trim(group)+1))
|
|
Cgroup = string2Cstring (group)
|
|
else
|
|
allocate (Cgroup(1))
|
|
Cgroup(1) = C_NULL_CHAR
|
|
end if
|
|
variable = lammps_actual_extract_variable (ptr, Cname, Cgroup)
|
|
deallocate (Cgroup)
|
|
end function lammps_extract_variable_Cptr
|
|
subroutine lammps_extract_variable_dp (variable, ptr, name, group)
|
|
real (C_double), intent(out) :: variable
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
character (len=*), intent(in), optional :: group
|
|
type (C_ptr) :: Cptr
|
|
real (C_double), pointer :: Fptr
|
|
if ( present(group) ) then
|
|
Cptr = lammps_extract_variable_Cptr (ptr, name, group)
|
|
else
|
|
Cptr = lammps_extract_variable_Cptr (ptr, name)
|
|
end if
|
|
call C_F_pointer (Cptr, Fptr)
|
|
variable = Fptr
|
|
nullify (Fptr)
|
|
call lammps_free (Cptr)
|
|
end subroutine lammps_extract_variable_dp
|
|
subroutine lammps_extract_variable_dpa (variable, ptr, name, group)
|
|
real (C_double), dimension(:), allocatable, intent(out) :: variable
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
character (len=*), intent(in), optional :: group
|
|
type (C_ptr) :: Cptr
|
|
real (C_double), dimension(:), pointer :: Fptr
|
|
integer :: natoms
|
|
if ( present(group) ) then
|
|
Cptr = lammps_extract_variable_Cptr (ptr, name, group)
|
|
else
|
|
Cptr = lammps_extract_variable_Cptr (ptr, name)
|
|
end if
|
|
natoms = lammps_get_natoms (ptr)
|
|
allocate (variable(natoms))
|
|
call C_F_pointer (Cptr, Fptr, (/natoms/))
|
|
variable = Fptr
|
|
nullify (Fptr)
|
|
call lammps_free (Cptr)
|
|
end subroutine lammps_extract_variable_dpa
|
|
|
|
!-------------------------------------------------------------------------2}}}
|
|
|
|
subroutine lammps_gather_atoms_ia (ptr, name, count, data)
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
integer, intent(in) :: count
|
|
integer, dimension(:), allocatable, intent(out) :: data
|
|
type (C_ptr) :: Cdata
|
|
integer (C_int), dimension(:), pointer :: Fdata
|
|
integer (C_int) :: natoms
|
|
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
|
|
integer (C_int), parameter :: Ctype = 0_C_int
|
|
integer (C_int) :: Ccount
|
|
natoms = lammps_get_natoms (ptr)
|
|
Cname = string2Cstring (name)
|
|
if ( count /= 1 .and. count /= 3 ) then
|
|
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
|
|
& count to be either 1 or 3')
|
|
else
|
|
Ccount = count
|
|
end if
|
|
allocate ( Fdata(count*natoms) )
|
|
allocate ( data(count*natoms) )
|
|
Cdata = C_loc (Fdata(1))
|
|
call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
|
|
data = Fdata
|
|
deallocate (Fdata)
|
|
end subroutine lammps_gather_atoms_ia
|
|
subroutine lammps_gather_atoms_dpa (ptr, name, count, data)
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
integer, intent(in) :: count
|
|
double precision, dimension(:), allocatable, intent(out) :: data
|
|
type (C_ptr) :: Cdata
|
|
real (C_double), dimension(:), pointer :: Fdata
|
|
integer (C_int) :: natoms
|
|
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
|
|
integer (C_int), parameter :: Ctype = 1_C_int
|
|
integer (C_int) :: Ccount
|
|
natoms = lammps_get_natoms (ptr)
|
|
Cname = string2Cstring (name)
|
|
if ( count /= 1 .and. count /= 3 ) then
|
|
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
|
|
& count to be either 1 or 3')
|
|
else
|
|
Ccount = count
|
|
end if
|
|
allocate ( Fdata(count*natoms) )
|
|
allocate ( data(count*natoms) )
|
|
Cdata = C_loc (Fdata(1))
|
|
call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
|
|
data = Fdata(:)
|
|
deallocate (Fdata)
|
|
end subroutine lammps_gather_atoms_dpa
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine lammps_scatter_atoms_ia (ptr, name, data)
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
integer, dimension(:), intent(in) :: data
|
|
integer (kind=C_int) :: natoms, Ccount
|
|
integer (kind=C_int), parameter :: Ctype = 0_C_int
|
|
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
|
|
integer (C_int), dimension(size(data)), target :: Fdata
|
|
type (C_ptr) :: Cdata
|
|
natoms = lammps_get_natoms (ptr)
|
|
Cname = string2Cstring (name)
|
|
Ccount = size(data) / natoms
|
|
if ( Ccount /= 1 .and. Ccount /= 3 ) &
|
|
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
|
|
& count to be either 1 or 3')
|
|
Fdata = data
|
|
Cdata = C_loc (Fdata(1))
|
|
call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
|
|
end subroutine lammps_scatter_atoms_ia
|
|
subroutine lammps_scatter_atoms_dpa (ptr, name, data)
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: name
|
|
double precision, dimension(:), intent(in) :: data
|
|
integer (kind=C_int) :: natoms, Ccount
|
|
integer (kind=C_int), parameter :: Ctype = 1_C_int
|
|
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
|
|
real (C_double), dimension(size(data)), target :: Fdata
|
|
type (C_ptr) :: Cdata
|
|
natoms = lammps_get_natoms (ptr)
|
|
Cname = string2Cstring (name)
|
|
Ccount = size(data) / natoms
|
|
if ( Ccount /= 1 .and. Ccount /= 3 ) &
|
|
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
|
|
& count to be either 1 or 3')
|
|
Fdata = data
|
|
Cdata = C_loc (Fdata(1))
|
|
call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
|
|
end subroutine lammps_scatter_atoms_dpa
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
function lammps_extract_compute_vectorsize (ptr, id, style) &
|
|
result (vectorsize)
|
|
integer :: vectorsize
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style
|
|
integer (C_int) :: Cvectorsize, Cstyle
|
|
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
|
|
Cid = string2Cstring (id)
|
|
Cstyle = int(style, C_int)
|
|
Cvectorsize = lammps_actual_extract_compute_vectorsize (ptr, Cid, Cstyle)
|
|
vectorsize = int(Cvectorsize, kind(vectorsize))
|
|
end function lammps_extract_compute_vectorsize
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
function lammps_extract_fix_vectorsize (ptr, id, style) &
|
|
result (vectorsize)
|
|
integer :: vectorsize
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style
|
|
integer (C_int) :: Cvectorsize, Cstyle
|
|
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
|
|
Cid = string2Cstring (id)
|
|
Cstyle = int(style, C_int)
|
|
Cvectorsize = lammps_actual_extract_fix_vectorsize (ptr, Cid, Cstyle)
|
|
vectorsize = int(Cvectorsize, kind(vectorsize))
|
|
end function lammps_extract_fix_vectorsize
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine lammps_extract_compute_arraysize (ptr, id, style, nrows, ncols)
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style
|
|
integer, intent(out) :: nrows, ncols
|
|
integer (C_int) :: Cstyle, Cnrows, Cncols
|
|
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
|
|
Cid = string2Cstring (id)
|
|
Cstyle = int (style, C_int)
|
|
call lammps_actual_extract_compute_arraysize (ptr, Cid, Cstyle, &
|
|
Cnrows, Cncols)
|
|
nrows = int (Cnrows, kind(nrows))
|
|
ncols = int (Cncols, kind(ncols))
|
|
end subroutine lammps_extract_compute_arraysize
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine lammps_extract_fix_arraysize (ptr, id, style, nrows, ncols)
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: id
|
|
integer, intent(in) :: style
|
|
integer, intent(out) :: nrows, ncols
|
|
integer (C_int) :: Cstyle, Cnrows, Cncols
|
|
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
|
|
Cid = string2Cstring (id)
|
|
Cstyle = int (style, kind(Cstyle))
|
|
call lammps_actual_extract_fix_arraysize (ptr, Cid, Cstyle, &
|
|
Cnrows, Cncols)
|
|
nrows = int (Cnrows, kind(nrows))
|
|
ncols = int (Cncols, kind(ncols))
|
|
end subroutine lammps_extract_fix_arraysize
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine lammps_error_all (ptr, file, line, str)
|
|
type (C_ptr), intent(in) :: ptr
|
|
character (len=*), intent(in) :: file, str
|
|
integer, intent(in) :: line
|
|
character (kind=C_char), dimension(len_trim(file)+1) :: Cfile
|
|
character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
|
|
integer (C_int) :: Cline
|
|
Cline = int(line, kind(Cline))
|
|
Cfile = string2Cstring (file)
|
|
Cstr = string2Cstring (str)
|
|
call lammps_actual_error_all (ptr, Cfile, Cline, Cstr)
|
|
end subroutine lammps_error_all
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
! Locally defined helper functions {{{1
|
|
|
|
pure function string2Cstring (string) result (C_string)
|
|
use, intrinsic :: ISO_C_binding, only : C_char, C_NULL_CHAR
|
|
character (len=*), intent(in) :: string
|
|
character (len=1, kind=C_char) :: C_string (len_trim(string)+1)
|
|
integer :: i, n
|
|
n = len_trim (string)
|
|
forall (i = 1:n)
|
|
C_string(i) = string(i:i)
|
|
end forall
|
|
C_string(n+1) = C_NULL_CHAR
|
|
end function string2Cstring
|
|
|
|
!-----------------------------------------------------------------------------
|
|
|
|
subroutine Cstring2argcargv (Cstring, argc, argv)
|
|
!! Converts a C-style string to argc and argv, that is, words in Cstring
|
|
!! become C-style strings in argv. IMPORTANT: Cstring is modified by
|
|
!! this routine! I would make Cstring local TO this routine and accept
|
|
!! a Fortran-style string instead, but we run into scoping and
|
|
!! allocation problems that way. This routine assumes the string is
|
|
!! null-terminated, as all C-style strings must be.
|
|
|
|
character (kind=C_char), dimension(*), target, intent(inout) :: Cstring
|
|
integer (C_int), intent(out) :: argc
|
|
type (C_ptr), dimension(:), allocatable, intent(out) :: argv
|
|
|
|
integer :: StringStart, SpaceIndex, strlen, argnum
|
|
|
|
argc = 1_C_int
|
|
|
|
! Find the length of the string
|
|
strlen = 1
|
|
do while ( Cstring(strlen) /= C_NULL_CHAR )
|
|
strlen = strlen + 1
|
|
end do
|
|
|
|
! Find the number of non-escaped spaces
|
|
SpaceIndex = 2
|
|
do while ( SpaceIndex < strlen )
|
|
if ( Cstring(SpaceIndex) == ' ' .and. &
|
|
Cstring(SpaceIndex-1) /= '\' ) then
|
|
argc = argc + 1_C_int
|
|
! Find the next non-space character
|
|
do while ( Cstring(SpaceIndex+1) == ' ')
|
|
SpaceIndex = SpaceIndex + 1
|
|
end do
|
|
end if
|
|
SpaceIndex = SpaceIndex + 1
|
|
end do
|
|
|
|
! Now allocate memory for argv
|
|
allocate (argv(argc))
|
|
|
|
! Now find the string starting and ending locations
|
|
StringStart = 1
|
|
SpaceIndex = 2
|
|
argnum = 1
|
|
do while ( SpaceIndex < strlen )
|
|
if ( Cstring(SpaceIndex) == ' ' .and. &
|
|
Cstring(SpaceIndex-1) /= '\' ) then
|
|
! Found a real space => split strings and store this one
|
|
Cstring(Spaceindex) = C_NULL_CHAR ! Replaces space with NULL
|
|
argv(argnum) = C_loc(Cstring(StringStart))
|
|
argnum = argnum + 1
|
|
! Find the next non-space character
|
|
do while ( Cstring(SpaceIndex+1) == ' ')
|
|
SpaceIndex = SpaceIndex + 1
|
|
end do
|
|
StringStart = SpaceIndex + 1
|
|
else if ( Cstring(SpaceIndex) == ' ' .and. &
|
|
Cstring(SpaceIndex-1) == '\' ) then
|
|
! Escaped space => remove backslash and move rest of array
|
|
Cstring(SpaceIndex-1:strlen-1) = Cstring(SpaceIndex:strlen)
|
|
strlen = strlen - 1 ! Last character is still C_NULL_CHAR
|
|
end if
|
|
SpaceIndex = SpaceIndex + 1
|
|
end do
|
|
! Now handle the last argument
|
|
argv(argnum) = C_loc(Cstring(StringStart))
|
|
|
|
end subroutine Cstring2argcargv
|
|
|
|
! 1}}}
|
|
|
|
end module LAMMPS
|
|
|
|
! vim: foldmethod=marker tabstop=3 softtabstop=3 shiftwidth=3 expandtab
|