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implemented create_atoms and encode_image_flags and unit tests for them; added IMGMASK and friends to extract_setting and unit tests for them; wrote documentation for them

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This commit is contained in:
Karl Hammond
2022-10-19 18:40:12 -05:00
parent 9a732ba513
commit b51c50294e
7 changed files with 578 additions and 53 deletions
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102
doc/src/Fortran.rst
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@ -146,9 +146,9 @@ Below is a small demonstration of the uses of the different functions:
PROGRAM testcmd
USE LIBLAMMPS
TYPE(lammps) :: lmp
CHARACTER(len=512) :: cmds
CHARACTER(len=40), ALLOCATABLE :: cmdlist(:)
CHARACTER(len=10) :: trimmed
CHARACTER(LEN=512) :: cmds
CHARACTER(LEN=40), ALLOCATABLE :: cmdlist(:)
CHARACTER(LEN=10) :: trimmed
INTEGER :: i
lmp = lammps()
@ -265,6 +265,7 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
:f subroutine gather_atoms_subset: :f:func:`gather_atoms_subset`
:f subroutine scatter_atoms: :f:func:`scatter_atoms`
:f subroutine scatter_atoms_subset: :f:func:`scatter_atoms_subset`
:f subroutine create_atoms: :f:func:`create_atoms`
:f function version: :f:func:`version`
:f subroutine flush_buffers: :f:func:`flush_buffers`
:f function is_running: :f:func:`is_running`
@ -1267,6 +1268,56 @@ Procedures Bound to the lammps Derived Type
--------
.. f:subroutine:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
This method calls :c:func:`lammps_create_atoms` to create additional atoms
from a given list of coordinates and a list of atom types. Additionally,
the atom IDs, velocities, and image flags may be provided.
.. versionadded:: TBD
:p integer(c_int) type [dimension(N)]: vector of :math:`N` atom types
(required/see note below)
:p real(c_double) x [dimension(3N)]: vector of :math:`3N` x/y/z positions
of the new atoms, arranged as :math:`[x_1,y_1,z_1,x_2,y_2,\dotsc]`
(required/see note below)
:o integer(\*) id [dimension(N)]: vector of :math:`N` atom IDs; if
absent, LAMMPS will generate them for you. \*The kind parameter should be
``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which
case it should be ``c_int64_t``.
:o real(c_double) v [dimension(3N)]: vector of :math:`3N` x/y/z velocities
of the new atoms, arranged as :math:`[v_{1,x},v_{1,y},v_{1,z},v_{2,x},
\dotsc]`; if absent, they will be set to zero
:o integer(\*) image [dimension(N)]: vector of :math:`N` image flags; if
absent, they are set to zero. \*The kind parameter should be
``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which
case it should be ``c_int64_t``. See note below.
:o logical bexpand: if ``.TRUE.``, atoms outside of shrink-wrap boundaries
will be created, not dropped, and the box dimensions will be extended.
Default is ``.FALSE.``
.. note::
The *type* and *x* arguments are required, but they are declared
``OPTIONAL`` in the module because making them mandatory would require
*id* to be present as well. To have LAMMPS generate the ids for you,
use a call something like
.. code-block:: Fortran
lmp%create_atoms(type=new_types, x=new_xs)
.. note::
When LAMMPS has been compiled with ``-DLAMMPS_BIGBIG``, it is not
possible to include the *image* parameter but omit the *id* parameter.
Either *id* must be present, or both *id* and *image* must be absent.
This is required because having all arguments be optional in both
generic functions creates an ambiguous interface. This limitation does
not exist if LAMMPS was not compiled with ``-DLAMMPS_BIGBIG``.
--------
.. f:function:: version()
This method returns the numeric LAMMPS version like
@ -1456,6 +1507,51 @@ Procedures Bound to the lammps Derived Type
--------
.. f:function:: encode_image_flags(ix, iy, iz)
Encodes three integer image flags into a single imageint.
.. versionadded:: TBD
This function performs the bit-shift, addition, and bit-wise OR operations
necessary to combine the values of three integers representing the image
flags in the :math:`x`-, :math:`y`-, and :math:`z`-directions. Unless LAMMPS
is compiled with ``-DLAMMPS_BIGBIG``, those integers are limited to 10-bit
signed integers :math:`[-512,512]`. If ``-DLAMMPS_BIGBIG`` was used when
compiling, then the return value is of kind ``c_int64_t`` instead of
kind ``c_int``, and the valid range for the individual image flags becomes
:math:`[-1048576,1048575]` (i.e., the range of a 21-bit signed integer).
There is no check on whether the arguments conform to these requirements.
:p integer(c_int) ix: image flag in :math:`x`-direction
:p integer(c_int) iy: image flag in :math:`y`-direction
:p integer(c_int) iz: image flag in :math:`z`-direction
:r integer(\*): encoded image flag. \*Kind parameter is ``c_int`` unless
LAMMPS was built with ``-DLAMMPS_BIGBIG``, in which case it is
``c_int64_t``.
.. note::
The fact that the programmer does not know the kind parameter of the
return value until compile time means that it is impossible to define an
interface that works for both sizes of ``imageint``. One side effect of
this is that you must assign the return value of this function to a
variable; it cannot be used as the argument to another function or as part
of an array constructor. For example,
.. code-block:: Fortran
my_images = [lmp%encode_image_flags(0,0,0), lmp%encode_image_flags(1,0,0)]
will *not* work; instead, do something like
.. code-block:: Fortran
my_images(1) = lmp%encode_image_flags(0,0,0)
my_images(2) = lmp%encode_image_flags(1,0,0)
--------
.. f:subroutine:: flush_buffers()
This function calls :cpp:func:`lammps_flush_buffers`, which flushes buffered

148
fortran/lammps.f90
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@ -142,6 +142,7 @@ MODULE LIBLAMMPS
PROCEDURE, NOPASS :: config_package_count => lammps_config_package_count
PROCEDURE, NOPASS :: config_package_name => lmp_config_package_name
PROCEDURE, NOPASS :: installed_packages => lmp_installed_packages
PROCEDURE :: encode_image_flags => lmp_encode_image_flags
!
PROCEDURE :: flush_buffers => lmp_flush_buffers
PROCEDURE :: is_running => lmp_is_running
@ -202,6 +203,11 @@ MODULE LIBLAMMPS
CHARACTER(LEN=:), ALLOCATABLE :: str
END TYPE lammps_variable_data
TYPE, EXTENDS(lammps_data_baseclass) :: lammps_image_data
INTEGER(c_int) :: i32
INTEGER(c_int64_t) :: i64
END TYPE lammps_image_data
! This overloads the assignment operator (=) so that assignments of the
! form
! nlocal = extract_global('nlocal')
@ -222,6 +228,9 @@ MODULE LIBLAMMPS
MODULE PROCEDURE assign_double_to_lammps_variable_data, &
assign_doublevec_to_lammps_variable_data, &
assign_string_to_lammps_variable_data
! Image data, too
MODULE PROCEDURE assign_int_to_lammps_image_data, &
assign_int64_to_lammps_image_data
END INTERFACE
! interface definitions for calling functions in library.cpp
@ -567,6 +576,10 @@ MODULE LIBLAMMPS
!INTEGER(c_int) FUNCTION lammps_plugin_count
!SUBROUTINE lammps_plugin_name
! We don't call lammps_encode_image_flags because its interface is
! ambiguous: we don't know sizeof(imageint) prior to compile time
! It is re-written in Fortran below. It was easier to do the same for
! lammps_decode_image_flags's equivalent.
!Both of these use LAMMPS_BIGBIG
!INTEGER(LAMMPS_imageint) FUNCTION lammps_encode_image_flags
!SUBROUTINE lammps_decode_image_flags
@ -1544,34 +1557,69 @@ CONTAINS
CALL lammps_free(Cname)
END SUBROUTINE lmp_scatter_atoms_subset_double
! equivalent function to lammps_create_atoms
! equivalent function to lammps_create_atoms (int ids or id absent)
SUBROUTINE lmp_create_atoms_int(self, id, type, x, v, image, bexpand)
CLASS(lammps), INTENT(IN) :: self
INTEGER(c_int), DIMENSION(:), TARGET :: id, image
INTEGER(c_int), DIMENSION(:), TARGET :: type
REAL(c_double), DIMENSION(:), TARGET :: x, v
LOGICAL :: bexpand
INTEGER(c_int), DIMENSION(:), TARGET, OPTIONAL :: id, image
INTEGER(c_int), DIMENSION(:), TARGET, OPTIONAL :: type
REAL(c_double), DIMENSION(:), TARGET, OPTIONAL :: x, v
LOGICAL, OPTIONAL :: bexpand
INTEGER(c_int) :: n, Cbexpand
TYPE(c_ptr) :: Cid, Ctype, Cx, Cv, Cimage
INTEGER(c_int) :: tagint_size, atoms_created
! type is actually NOT optional, but we can't make id optional without it,
! so we check at run-time
IF (.NOT. PRESENT(type)) THEN
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'the "type" argument to create_atoms is required&
& [Fortran/create_atoms]')
END IF
tagint_size = lmp_extract_setting(self, 'tagint')
IF ( tagint_size /= 4_c_int ) THEN
IF (tagint_size /= 4_c_int .AND. (PRESENT(id) .OR. PRESENT(image))) THEN
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'Unable to create_atoms; your id/image array types are incompatible&
& with LAMMPS_SMALLBIG and LAMMPS_SMALLSMALL [Fortran/create_atoms]')
RETURN ! in case exception is caught
END IF
n = SIZE(id, KIND=c_int)
n = SIZE(type, KIND=c_int)
IF (PRESENT(bexpand)) THEN
IF (bexpand) THEN
Cbexpand = 1_c_int
ELSE
Cbexpand = 0
Cbexpand = 0_c_int
END IF
ELSE
Cbexpand = 0_c_int
END IF
IF (PRESENT(id)) THEN
Cid = C_LOC(id(1))
ELSE
Cid = c_null_ptr
END IF
IF (PRESENT(type)) THEN
Ctype = C_LOC(type(1))
ELSE
RETURN ! We shouldn't get here unless exceptions are being caught
END IF
IF (PRESENT(image)) THEN
Cimage = C_LOC(image(1))
ELSE
Cimage = c_null_ptr
END IF
IF (PRESENT(x)) THEN
Cx = C_LOC(x(1))
ELSE
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'the argument "x" to create_atoms is required')
RETURN
END IF
IF (PRESENT(v)) THEN
Cv = C_LOC(v(1))
ELSE
Cv = c_null_ptr
END IF
atoms_created = lammps_create_atoms(self%handle, n, Cid, Ctype, Cx, Cv, &
Cimage, Cbexpand)
IF ( atoms_created < 0_c_int ) THEN
@ -1583,12 +1631,15 @@ CONTAINS
END IF
END SUBROUTINE lmp_create_atoms_int
! equivalent function to lammps_create_atoms (long int ids and images)
SUBROUTINE lmp_create_atoms_bigbig(self, id, type, x, v, image, bexpand)
CLASS(lammps), INTENT(IN) :: self
INTEGER(c_int64_t), DIMENSION(:), TARGET :: id, image
INTEGER(c_int64_t), DIMENSION(:), TARGET :: id
INTEGER(c_int), DIMENSION(:), TARGET :: type
REAL(c_double), DIMENSION(:), TARGET :: x, v
LOGICAL :: bexpand
REAL(c_double), DIMENSION(:), TARGET :: x
REAL(c_double), DIMENSION(:), OPTIONAL, TARGET :: v
INTEGER(c_int64_t), DIMENSION(:), OPTIONAL, TARGET :: image
LOGICAL, OPTIONAL :: bexpand
INTEGER(c_int) :: n, Cbexpand
TYPE(c_ptr) :: Cid, Ctype, Cx, Cv, Cimage
INTEGER(c_int) :: tagint_size, atoms_created
@ -1599,17 +1650,29 @@ CONTAINS
'Unable to create_atoms; your id/image array types are incompatible&
& with LAMMPS_BIGBIG')
END IF
n = SIZE(id, KIND=c_int)
n = SIZE(type, KIND=c_int)
IF (PRESENT(bexpand)) THEN
IF (bexpand) THEN
Cbexpand = 1_c_int
ELSE
Cbexpand = 0
Cbexpand = 0_c_int
END IF
ELSE
Cbexpand = 0_c_int
END IF
Cid = C_LOC(id(1))
Ctype = C_LOC(type(1))
IF (PRESENT(image)) THEN
Cimage = C_LOC(image(1))
ELSE
Cimage = c_null_ptr
END IF
Cx = C_LOC(x(1))
IF (PRESENT(v)) THEN
Cv = C_LOC(v(1))
ELSE
Cv = c_null_ptr
END IF
atoms_created = lammps_create_atoms(self%handle, n, Cid, Ctype, Cx, Cv, &
Cimage, Cbexpand)
IF ( atoms_created < 0_c_int ) THEN
@ -1748,6 +1811,43 @@ CONTAINS
END DO
END SUBROUTINE lmp_installed_packages
! equivalent function to lammps_encode_image_flags
FUNCTION lmp_encode_image_flags(self, ix, iy, iz) RESULT (image)
CLASS(lammps), INTENT(IN), TARGET :: self
INTEGER(c_int), INTENT(IN) :: ix, iy, iz
TYPE(lammps_image_data) :: image
INTEGER(c_int) :: imageint_size
INTEGER(c_int) :: IMGMAX, IMGMASK, IMGBITS, IMG2BITS
INTEGER(c_int64_t) :: ibx, iby, ibz, BIMGMAX, BIMGMASK, BIMGBITS, BIMG2BITS
image%lammps_instance => self
IMGMASK = lmp_extract_setting(self, 'IMGMASK')
IMGMAX = lmp_extract_setting(self, 'IMGMAX')
IMGBITS = lmp_extract_setting(self, 'IMGBITS')
IMG2BITS = lmp_extract_setting(self, 'IMG2BITS')
imageint_size = lmp_extract_setting(self, 'imageint')
IF (imageint_size == 4_c_int) THEN
image%datatype = DATA_INT
image%i32 = IOR( IOR(IAND(ix + IMGMAX, IMGMASK), &
ISHFT(IAND(iy + IMGMAX, IMGMASK), IMGBITS)), &
ISHFT(IAND(iz + IMGMAX, IMGMASK), IMG2BITS) )
ELSE
image%datatype = DATA_INT64
ibx = ix
iby = iy
ibz = iz
BIMGMAX = IMGMAX
BIMGMASK = IMGMASK
BIMGBITS = IMGBITS
BIMG2BITS = IMG2BITS
image%i64 = IOR( IOR(IAND(ibx + BIMGMAX, BIMGMASK), &
ISHFT(IAND(iby + BIMGMAX, BIMGMASK), BIMGBITS)), &
ISHFT(IAND(ibz + BIMGMAX, BIMGMASK), BIMG2BITS) )
END IF
END FUNCTION lmp_encode_image_flags
! equivalent function to lammps_decode_image_flags
! equivalent function to lammps_flush_buffers
SUBROUTINE lmp_flush_buffers(self)
CLASS(lammps), INTENT(IN) :: self
@ -1984,6 +2084,28 @@ CONTAINS
END IF
END SUBROUTINE assign_string_to_lammps_variable_data
SUBROUTINE assign_int_to_lammps_image_data(lhs, rhs)
INTEGER(c_int), INTENT(OUT) :: lhs
CLASS(lammps_image_data), INTENT(IN) :: rhs
IF (rhs%datatype == DATA_INT) THEN
lhs = rhs%i32
ELSE
CALL assignment_error(rhs, 'scalar int')
END IF
END SUBROUTINE assign_int_to_lammps_image_data
SUBROUTINE assign_int64_to_lammps_image_data(lhs, rhs)
INTEGER(c_int64_t), INTENT(OUT) :: lhs
CLASS(lammps_image_data), INTENT(IN) :: rhs
IF (rhs%datatype == DATA_INT64) THEN
lhs = rhs%i64
ELSE
CALL assignment_error(rhs, 'scalar long int')
END IF
END SUBROUTINE assign_int64_to_lammps_image_data
! ----------------------------------------------------------------------
! Generic function to catch all errors in assignments of LAMMPS data to
! user-space variables/pointers

28
src/library.cpp
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@ -953,6 +953,7 @@ not recognized, the function returns -1. The integer sizes functions may
be called without a valid LAMMPS object handle (it is ignored).
* :ref:`Integer sizes <extract_integer_sizes>`
* :ref:`Image masks <extract_image_masks>`
* :ref:`System status <extract_system_status>`
* :ref:`System sizes <extract_system_sizes>`
* :ref:`Atom style flags <extract_atom_flags>`
@ -977,6 +978,28 @@ be called without a valid LAMMPS object handle (it is ignored).
- size of the ``imageint`` integer type, 4 or 8 bytes.
Set at :ref:`compile time <size>`.
.. _extract_image_masks:
**Image masks**
These settings are related to how LAMMPS stores and interprets periodic images. The values are used
internally by the Fortran interface and are not likely to be useful to users.
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Description / Return value
* - IMGMASK
- Bit-mask used to convert image flags to a single integer
* - IMGMAX
- Maximum allowed image number for a particular atom
* - IMGBITS
- Bits used in image counts
* - IMG2BITS
- Second bitmask used in image counts
.. _extract_system_status:
**System status**
@ -1096,6 +1119,11 @@ int lammps_extract_setting(void *handle, const char *keyword)
if (strcmp(keyword,"tagint") == 0) return sizeof(tagint);
if (strcmp(keyword,"imageint") == 0) return sizeof(imageint);
if (strcmp(keyword,"IMGMASK") == 0) return IMGMASK;
if (strcmp(keyword,"IMGBITS") == 0) return IMGBITS;
if (strcmp(keyword,"IMG2BITS") == 0) return IMG2BITS;
if (strcmp(keyword,"IMGMAX") == 0) return IMGMAX;
if (strcmp(keyword,"dimension") == 0) return lmp->domain->dimension;
if (strcmp(keyword,"box_exist") == 0) return lmp->domain->box_exist;
if (strcmp(keyword,"newton_bond") == 0) return lmp->force->newton_bond;

99
unittest/fortran/test_fortran_create_atoms.f90
View File

@ -24,7 +24,7 @@ END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_create_atoms() BIND(C)
USE LIBLAMMPS
USE keepstuff, ONLY : lmp, big_input, cont_input, more_input
USE keepstuff, ONLY : lmp, big_input, cont_input, more_input, pair_input
IMPLICIT NONE
!CALL lmp%command('atom_modify map array')
@ -35,7 +35,7 @@ END SUBROUTINE f_lammps_setup_create_atoms
SUBROUTINE f_lammps_create_three_atoms() BIND(C)
USE ISO_C_BINDING, ONLY: c_double, c_int, c_int64_t
USE keepstuff, ONLY : lmp, big_input, cont_input, more_input
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), DIMENSION(3) :: new_ids, new_images, new_types
@ -46,8 +46,16 @@ SUBROUTINE f_lammps_create_three_atoms() BIND(C)
new_ids = [4, 6, 5]
new_big_ids = [4, 6, 5]
new_images = [0, 0, 1]
new_big_images = [0, 0, 1]
tagint_size = lmp%extract_setting('tagint')
IF ( tagint_size == 4_c_int ) THEN
new_images(1) = lmp%encode_image_flags(1, -1, 3)
new_images(2) = lmp%encode_image_flags(-2, 0, 0)
new_images(3) = lmp%encode_image_flags(-2, -2, 1)
ELSE
new_big_images(1) = lmp%encode_image_flags(1, -1, 3)
new_big_images(2) = lmp%encode_image_flags(-2, 0, 0)
new_big_images(3) = lmp%encode_image_flags(-2, -2, 1)
END IF
new_types = [1, 1, 1]
new_x = [ 1.0_c_double, 1.8_c_double, 2.718281828_c_double, &
0.6_c_double, 0.8_c_double, 2.2_c_double, &
@ -56,7 +64,6 @@ SUBROUTINE f_lammps_create_three_atoms() BIND(C)
0.1_c_double, 0.2_c_double, -0.2_c_double, &
1.0_c_double, -1.0_c_double, 3.0_c_double ]
wrap = .FALSE.
tagint_size = lmp%extract_setting('tagint')
IF ( tagint_size == 4_c_int ) THEN
CALL lmp%create_atoms(new_ids, new_types, new_x, new_v, new_images, wrap)
ELSE
@ -65,4 +72,86 @@ SUBROUTINE f_lammps_create_three_atoms() BIND(C)
END IF
END SUBROUTINE f_lammps_create_three_atoms
SUBROUTINE f_lammps_create_two_more() BIND(C)
USE ISO_C_BINDING, ONLY: c_double, c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), DIMENSION(2) :: new_types
REAL(c_double), DIMENSION(6) :: new_x
new_types = [1_c_int, 1_c_int]
new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, &
1.2_c_double, 2.1_c_double, 1.25_c_double]
CALL lmp%create_atoms(type=new_types, x=new_x)
END SUBROUTINE f_lammps_create_two_more
SUBROUTINE f_lammps_create_two_more_small() BIND(C)
USE ISO_C_BINDING, ONLY: c_double, c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), DIMENSION(2) :: new_types
REAL(c_double), DIMENSION(6) :: new_x
INTEGER(c_int), DIMENSION(2) :: new_id, new_image
new_types = [1_c_int, 1_c_int]
new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, &
1.2_c_double, 2.1_c_double, 1.25_c_double]
new_id = [8_c_int, 7_c_int]
new_image(1) = lmp%encode_image_flags(1,0,0)
new_image(2) = lmp%encode_image_flags(-1,0,0)
CALL lmp%create_atoms(id=new_id, image=new_image, type=new_types, x=new_x)
END SUBROUTINE f_lammps_create_two_more_small
SUBROUTINE f_lammps_create_two_more_big() BIND(C)
USE ISO_C_BINDING, ONLY: c_double, c_int, c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), DIMENSION(2) :: new_types
REAL(c_double), DIMENSION(6) :: new_x
INTEGER(c_int64_t), DIMENSION(2) :: new_id, new_image
new_types = [1_c_int, 1_c_int]
new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, &
1.2_c_double, 2.1_c_double, 1.25_c_double]
new_id = [8_c_int64_t, 7_c_int64_t]
new_image(1) = lmp%encode_image_flags(1,0,0)
new_image(2) = lmp%encode_image_flags(-1,0,0)
CALL lmp%create_atoms(id=new_id, image=new_image, type=new_types, x=new_x)
END SUBROUTINE f_lammps_create_two_more_big
SUBROUTINE f_lammps_create_two_more_small2() BIND(C)
USE ISO_C_BINDING, ONLY: c_double, c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), DIMENSION(2) :: new_types
REAL(c_double), DIMENSION(6) :: new_x
INTEGER(c_int), DIMENSION(2) :: new_id
new_types = [1_c_int, 1_c_int]
new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, &
1.2_c_double, 2.1_c_double, 1.25_c_double]
new_id = [8_c_int, 7_c_int]
CALL lmp%create_atoms(id=new_id, type=new_types, x=new_x)
END SUBROUTINE f_lammps_create_two_more_small2
SUBROUTINE f_lammps_create_two_more_big2() BIND(C)
USE ISO_C_BINDING, ONLY: c_double, c_int, c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), DIMENSION(2) :: new_types
REAL(c_double), DIMENSION(6) :: new_x
INTEGER(c_int64_t), DIMENSION(2) :: new_id
new_types = [1_c_int, 1_c_int]
new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, &
1.2_c_double, 2.1_c_double, 1.25_c_double]
new_id = [8_c_int64_t, 7_c_int64_t]
CALL lmp%create_atoms(id=new_id, type=new_types, x=new_x)
END SUBROUTINE f_lammps_create_two_more_big2
! vim: ts=2 sts=2 sw=2 et

31
unittest/fortran/test_fortran_properties.f90
View File

@ -29,7 +29,7 @@ FUNCTION f_lammps_get_mpi_comm() BIND(C)
END FUNCTION f_lammps_get_mpi_comm
FUNCTION f_lammps_extract_setting(Cstr) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char, c_null_char
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
@ -39,7 +39,7 @@ FUNCTION f_lammps_extract_setting(Cstr) BIND(C)
CHARACTER(LEN=:), ALLOCATABLE :: Fstr
i = 1
DO WHILE (Cstr(i) /= ACHAR(0))
DO WHILE (Cstr(i) /= c_null_char)
i = i + 1
END DO
strlen = i
@ -66,7 +66,8 @@ FUNCTION f_lammps_has_error() BIND(C)
END FUNCTION f_lammps_has_error
FUNCTION f_lammps_get_last_error_message(errmesg, errlen) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char, c_ptr, C_F_POINTER
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char, c_ptr, C_F_POINTER, &
c_null_char
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
@ -83,7 +84,29 @@ FUNCTION f_lammps_get_last_error_message(errmesg, errlen) BIND(C)
! and copy to C style string
DO i=1, errlen
errmesg(i) = buffer(i:i)
IF (buffer(i:i) == ACHAR(0)) EXIT
IF (buffer(i:i) == c_null_char) EXIT
END DO
DEALLOCATE(buffer)
END FUNCTION f_lammps_get_last_error_message
FUNCTION f_lammps_get_image_flags_int(ix, iy, iz) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: ix, iy, iz
INTEGER(c_int) :: f_lammps_get_image_flags_int
f_lammps_get_image_flags_int = lmp%encode_image_flags(ix, iy, iz)
END FUNCTION f_lammps_get_image_flags_int
FUNCTION f_lammps_get_image_flags_bigint(ix, iy, iz) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_int64_t
USE keepstuff, ONLY : lmp
USE LIBLAMMPS
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: ix, iy, iz
INTEGER(c_int64_t) :: f_lammps_get_image_flags_bigint
f_lammps_get_image_flags_bigint = lmp%encode_image_flags(ix, iy, iz)
END FUNCTION f_lammps_get_image_flags_bigint

144
unittest/fortran/wrap_create_atoms.cpp
View File

@ -16,6 +16,11 @@ void *f_lammps_with_args();
void f_lammps_close();
void f_lammps_setup_create_atoms();
void f_lammps_create_three_atoms();
void f_lammps_create_two_more();
void f_lammps_create_two_more_small();
void f_lammps_create_two_more_big();
void f_lammps_create_two_more_small2();
void f_lammps_create_two_more_big2();
}
class LAMMPS_create_atoms : public ::testing::Test {
@ -41,7 +46,7 @@ protected:
}
};
TEST_F(LAMMPS_create_atoms, create_two)
TEST_F(LAMMPS_create_atoms, create_three)
{
f_lammps_setup_create_atoms();
#ifdef LAMMPS_BIGBIG
@ -61,7 +66,7 @@ TEST_F(LAMMPS_create_atoms, create_two)
EXPECT_EQ(lmp->atom->nlocal, 6);
for (int i = 0; i < lmp->atom->nlocal; i++) {
if (tag[i] == 4) {
EXPECT_EQ(image[i],0);
EXPECT_EQ(image[i],lammps_encode_image_flags(1,-1,3));
EXPECT_DOUBLE_EQ(x[i][0],1.0);
EXPECT_DOUBLE_EQ(x[i][1],1.8);
EXPECT_DOUBLE_EQ(x[i][2],2.718281828);
@ -70,7 +75,7 @@ TEST_F(LAMMPS_create_atoms, create_two)
EXPECT_DOUBLE_EQ(v[i][2],-1.0);
}
if (tag[i] == 5) {
EXPECT_EQ(image[i],1);
EXPECT_EQ(image[i],lammps_encode_image_flags(-2,-2,1));
EXPECT_DOUBLE_EQ(x[i][0],1.8);
EXPECT_DOUBLE_EQ(x[i][1],0.1);
EXPECT_DOUBLE_EQ(x[i][2],1.8);
@ -79,7 +84,7 @@ TEST_F(LAMMPS_create_atoms, create_two)
EXPECT_DOUBLE_EQ(v[i][2],3.0);
}
if (tag[i] == 6) {
EXPECT_EQ(image[i],0);
EXPECT_EQ(image[i],lammps_encode_image_flags(-2,0,0));
EXPECT_DOUBLE_EQ(x[i][0],0.6);
EXPECT_DOUBLE_EQ(x[i][1],0.8);
EXPECT_DOUBLE_EQ(x[i][2],2.2);
@ -89,3 +94,134 @@ TEST_F(LAMMPS_create_atoms, create_two)
}
}
};
TEST_F(LAMMPS_create_atoms, create_two_more)
{
f_lammps_setup_create_atoms();
#ifdef LAMMPS_BIGBIG
int64_t *tag, *image;
#else
int *tag, *image;
#endif
int *type;
double **x, **v;
f_lammps_create_three_atoms();
EXPECT_EQ(lmp->atom->nlocal, 6);
f_lammps_create_two_more();
EXPECT_EQ(lmp->atom->nlocal, 8);
tag = lmp->atom->tag;
image = lmp->atom->image;
x = lmp->atom->x;
v = lmp->atom->v;
type = lmp->atom->type;
for (int i = 0; i < lmp->atom->nlocal; i++) {
if (tag[i] == 7) {
EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0));
EXPECT_DOUBLE_EQ(x[i][0],0.1);
EXPECT_DOUBLE_EQ(x[i][1],1.9);
EXPECT_DOUBLE_EQ(x[i][2],3.8);
EXPECT_DOUBLE_EQ(v[i][0],0.0);
EXPECT_DOUBLE_EQ(v[i][1],0.0);
EXPECT_DOUBLE_EQ(v[i][2],0.0);
}
if (tag[i] == 8) {
EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0));
EXPECT_DOUBLE_EQ(x[i][0],1.2);
EXPECT_DOUBLE_EQ(x[i][1],2.1);
EXPECT_DOUBLE_EQ(x[i][2],1.25);
EXPECT_DOUBLE_EQ(v[i][0],0.0);
EXPECT_DOUBLE_EQ(v[i][1],0.0);
EXPECT_DOUBLE_EQ(v[i][2],0.0);
}
}
};
TEST_F(LAMMPS_create_atoms, create_two_more_bigsmall)
{
f_lammps_setup_create_atoms();
#ifdef LAMMPS_BIGBIG
int64_t *tag, *image;
#else
int *tag, *image;
#endif
int *type;
double **x, **v;
f_lammps_create_three_atoms();
EXPECT_EQ(lmp->atom->nlocal, 6);
#ifdef LAMMPS_BIGBIG
f_lammps_create_two_more_big();
#else
f_lammps_create_two_more_small();
#endif
EXPECT_EQ(lmp->atom->nlocal, 8);
tag = lmp->atom->tag;
image = lmp->atom->image;
x = lmp->atom->x;
v = lmp->atom->v;
type = lmp->atom->type;
for (int i = 0; i < lmp->atom->nlocal; i++) {
if (tag[i] == 7) {
EXPECT_EQ(image[i],lammps_encode_image_flags(-1,0,0));
EXPECT_DOUBLE_EQ(x[i][0],1.2);
EXPECT_DOUBLE_EQ(x[i][1],2.1);
EXPECT_DOUBLE_EQ(x[i][2],1.25);
EXPECT_DOUBLE_EQ(v[i][0],0.0);
EXPECT_DOUBLE_EQ(v[i][1],0.0);
EXPECT_DOUBLE_EQ(v[i][2],0.0);
}
if (tag[i] == 8) {
EXPECT_EQ(image[i],lammps_encode_image_flags(1,0,0));
EXPECT_DOUBLE_EQ(x[i][0],0.1);
EXPECT_DOUBLE_EQ(x[i][1],1.9);
EXPECT_DOUBLE_EQ(x[i][2],3.8);
EXPECT_DOUBLE_EQ(v[i][0],0.0);
EXPECT_DOUBLE_EQ(v[i][1],0.0);
EXPECT_DOUBLE_EQ(v[i][2],0.0);
}
}
};
TEST_F(LAMMPS_create_atoms, create_two_more_bigsmall2)
{
f_lammps_setup_create_atoms();
#ifdef LAMMPS_BIGBIG
int64_t *tag, *image;
#else
int *tag, *image;
#endif
int *type;
double **x, **v;
f_lammps_create_three_atoms();
EXPECT_EQ(lmp->atom->nlocal, 6);
#ifdef LAMMPS_BIGBIG
f_lammps_create_two_more_big2();
#else
f_lammps_create_two_more_small2();
#endif
EXPECT_EQ(lmp->atom->nlocal, 8);
tag = lmp->atom->tag;
image = lmp->atom->image;
x = lmp->atom->x;
v = lmp->atom->v;
type = lmp->atom->type;
for (int i = 0; i < lmp->atom->nlocal; i++) {
if (tag[i] == 7) {
EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0));
EXPECT_DOUBLE_EQ(x[i][0],1.2);
EXPECT_DOUBLE_EQ(x[i][1],2.1);
EXPECT_DOUBLE_EQ(x[i][2],1.25);
EXPECT_DOUBLE_EQ(v[i][0],0.0);
EXPECT_DOUBLE_EQ(v[i][1],0.0);
EXPECT_DOUBLE_EQ(v[i][2],0.0);
}
if (tag[i] == 8) {
EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0));
EXPECT_DOUBLE_EQ(x[i][0],0.1);
EXPECT_DOUBLE_EQ(x[i][1],1.9);
EXPECT_DOUBLE_EQ(x[i][2],3.8);
EXPECT_DOUBLE_EQ(v[i][0],0.0);
EXPECT_DOUBLE_EQ(v[i][1],0.0);
EXPECT_DOUBLE_EQ(v[i][2],0.0);
}
}
};

31
unittest/fortran/wrap_properties.cpp
View File

@ -3,6 +3,7 @@
#include "lammps.h"
#include "library.h"
#include <cstdint>
#include <string>
#include "gmock/gmock.h"
@ -18,6 +19,8 @@ int f_lammps_get_mpi_comm();
int f_lammps_extract_setting(const char *);
int f_lammps_has_error();
int f_lammps_get_last_error_message(char *, int);
int f_lammps_get_image_flags_int(int, int, int);
int64_t f_lammps_get_image_flags_bigint(int, int, int);
}
namespace LAMMPS_NS {
@ -85,9 +88,17 @@ TEST_F(LAMMPS_properties, extract_setting)
#if defined(LAMMPS_BIGBIG)
EXPECT_EQ(f_lammps_extract_setting("tagint"), 8);
EXPECT_EQ(f_lammps_extract_setting("imageint"), 8);
EXPECT_EQ(f_lammps_extract_setting("IMGMASK"), 2097151);
EXPECT_EQ(f_lammps_extract_setting("IMGMAX"), 1048576);
EXPECT_EQ(f_lammps_extract_setting("IMGBITS"), 21);
EXPECT_EQ(f_lammps_extract_setting("IMG2BITS"), 42);
#else
EXPECT_EQ(f_lammps_extract_setting("tagint"), 4);
EXPECT_EQ(f_lammps_extract_setting("imageint"), 4);
EXPECT_EQ(f_lammps_extract_setting("IMGMASK"), 1023);
EXPECT_EQ(f_lammps_extract_setting("IMGMAX"), 512);
EXPECT_EQ(f_lammps_extract_setting("IMGBITS"), 10);
EXPECT_EQ(f_lammps_extract_setting("IMG2BITS"), 20);
#endif
EXPECT_EQ(f_lammps_extract_setting("box_exist"), 0);
@ -141,4 +152,24 @@ TEST_F(LAMMPS_properties, has_error)
EXPECT_EQ(err, 0);
EXPECT_THAT(errmsg, ContainsRegex(" "));
};
TEST_F(LAMMPS_properties, get_image_flags)
{
#ifdef LAMMPS_BIGBIG
int64_t image = f_lammps_get_image_flags_bigint(0,0,0);
int64_t Cimage = lammps_encode_image_flags(0,0,0);
EXPECT_EQ(image, Cimage);
image = f_lammps_get_image_flags_bigint(1,-1,1);
Cimage = lammps_encode_image_flags(1,-1,1);
EXPECT_EQ(image, Cimage);
#else
int image = f_lammps_get_image_flags_int(0,0,0);
int Cimage = lammps_encode_image_flags(0,0,0);
EXPECT_EQ(image, Cimage);
image = f_lammps_get_image_flags_int(1,-1,1);
Cimage = lammps_encode_image_flags(1,-1,1);
EXPECT_EQ(image, Cimage);
#endif
}
} // namespace LAMMPS_NS