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Implemented extract_fix, extract_variable, flush_buffers; unit test for extract_fix

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This commit is contained in:
Karl Hammond
2022-09-28 22:09:26 -05:00
parent e22699197d
commit 1d4297e2dd
7 changed files with 597 additions and 50 deletions
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350
fortran/lammps.f90
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@ -65,7 +65,10 @@ MODULE LIBLAMMPS
LMP_ERROR_ONE = 1, & ! call Error::one() (from this MPI rank) LMP_ERROR_ONE = 1, & ! call Error::one() (from this MPI rank)
LMP_ERROR_ALL = 2, & ! call Error::all() (from all MPI ranks) LMP_ERROR_ALL = 2, & ! call Error::all() (from all MPI ranks)
LMP_ERROR_WORLD = 4, & ! error on comm->world LMP_ERROR_WORLD = 4, & ! error on comm->world
LMP_ERROR_UNIVERSE = 8 ! error on comm->universe LMP_ERROR_UNIVERSE = 8, & ! error on comm->universe
LMP_VAR_EQUAL = 0, & ! equal-style variables (and compatible)
LMP_VAR_ATOM = 1, & ! atom-style variables (and compatible)
LMP_VAR_STRING = 2 ! string variables (and compatible)
! "Constants" to use with extract_compute and friends ! "Constants" to use with extract_compute and friends
TYPE lammps_style TYPE lammps_style
@ -97,11 +100,14 @@ MODULE LIBLAMMPS
PROCEDURE :: extract_global => lmp_extract_global PROCEDURE :: extract_global => lmp_extract_global
PROCEDURE :: extract_atom => lmp_extract_atom PROCEDURE :: extract_atom => lmp_extract_atom
PROCEDURE :: extract_compute => lmp_extract_compute PROCEDURE :: extract_compute => lmp_extract_compute
PROCEDURE :: extract_fix => lmp_extract_fix
PROCEDURE :: extract_variable => lmp_extract_variable
! !
PROCEDURE :: version => lmp_version PROCEDURE :: version => lmp_version
PROCEDURE :: is_running => lmp_is_running
! !
PROCEDURE :: flush_buffers => lmp_flush_buffers PROCEDURE :: flush_buffers => lmp_flush_buffers
PROCEDURE :: is_running => lmp_is_running
! force_timeout
PROCEDURE :: has_error => lmp_has_error PROCEDURE :: has_error => lmp_has_error
PROCEDURE :: get_last_error_message => lmp_get_last_error_message PROCEDURE :: get_last_error_message => lmp_get_last_error_message
END TYPE lammps END TYPE lammps
@ -118,10 +124,16 @@ MODULE LIBLAMMPS
ENUMERATOR :: DATA_STRING ENUMERATOR :: DATA_STRING
END ENUM END ENUM
! Base class for receiving LAMMPS data (to reduce code duplication)
TYPE lammps_data_baseclass
INTEGER(c_int) :: datatype = -1_c_int
! in case we need to call the Error class in an assignment
CLASS(lammps), POINTER, PRIVATE :: lammps_instance => NULL()
END TYPE lammps_data_baseclass
! Derived type for receiving LAMMPS data (in lieu of the ability to type cast ! Derived type for receiving LAMMPS data (in lieu of the ability to type cast
! pointers) ! pointers). Used for extract_compute, extract_atom
TYPE lammps_data TYPE, EXTENDS(lammps_data_baseclass) :: lammps_data
INTEGER(c_int) :: datatype
INTEGER(c_int), POINTER :: i32 => NULL() INTEGER(c_int), POINTER :: i32 => NULL()
INTEGER(c_int), DIMENSION(:), POINTER :: i32_vec => NULL() INTEGER(c_int), DIMENSION(:), POINTER :: i32_vec => NULL()
INTEGER(c_int64_t), POINTER :: i64 => NULL() INTEGER(c_int64_t), POINTER :: i64 => NULL()
@ -132,6 +144,26 @@ MODULE LIBLAMMPS
CHARACTER(LEN=:), ALLOCATABLE :: str CHARACTER(LEN=:), ALLOCATABLE :: str
END TYPE lammps_data END TYPE lammps_data
! Derived type for holding LAMMPS fix data
! Done this way because fix global data are not pointers, but computed
! on-the-fly, whereas per-atom and local data are pointers to the actual
! array. Doing it this way saves the user from having to explicitly
! deallocate all of the pointers.
TYPE, EXTENDS(lammps_data_baseclass) :: lammps_fix_data
REAL(c_double) :: r64
REAL(c_double), DIMENSION(:), POINTER :: r64_vec => NULL()
REAL(c_double), DIMENSION(:,:), POINTER :: r64_mat => NULL()
END TYPE lammps_fix_data
! Derived type for holding LAMMPS variable data
! Done this way because extract_variable calculates variable values, it does
! not return pointers to LAMMPS data.
TYPE, EXTENDS(lammps_data_baseclass) :: lammps_variable_data
REAL(c_double) :: r64
REAL(c_double), DIMENSION(:), ALLOCATABLE :: r64_vec
CHARACTER(LEN=:), ALLOCATABLE :: str
END TYPE lammps_variable_data
! This overloads the assignment operator (=) so that assignments of the ! This overloads the assignment operator (=) so that assignments of the
! form ! form
! nlocal = extract_global('nlocal') ! nlocal = extract_global('nlocal')
@ -144,6 +176,10 @@ MODULE LIBLAMMPS
assign_double_to_lammps_data, assign_doublevec_to_lammps_data, & assign_double_to_lammps_data, assign_doublevec_to_lammps_data, &
assign_doublemat_to_lammps_data, & assign_doublemat_to_lammps_data, &
assign_string_to_lammps_data assign_string_to_lammps_data
! We handle fix data (slightly) differently
MODULE PROCEDURE assign_double_to_lammps_fix_data, &
assign_doublevec_to_lammps_fix_data, &
assign_doublemat_to_lammps_fix_data
END INTERFACE END INTERFACE
! interface definitions for calling functions in library.cpp ! interface definitions for calling functions in library.cpp
@ -312,9 +348,27 @@ MODULE LIBLAMMPS
TYPE(c_ptr) :: lammps_extract_compute TYPE(c_ptr) :: lammps_extract_compute
END FUNCTION lammps_extract_compute END FUNCTION lammps_extract_compute
!(generic) lammps_extract_fix FUNCTION lammps_extract_fix(handle, id, style, type, nrow, ncol) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: handle, id
INTEGER(c_int), INTENT(IN), VALUE :: style, type, nrow, ncol
TYPE(c_ptr) :: lammps_extract_fix
END FUNCTION lammps_extract_fix
!(generic) lammps_extract_variable FUNCTION lammps_extract_variable_datatype(handle,name) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: handle, name
INTEGER(c_int) :: lammps_extract_variable_datatype
END FUNCTION lammps_extract_variable_datatype
FUNCTION lammps_extract_variable(handle, name, group) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: handle, name, group
TYPE(c_ptr) :: lammps_extract_variable
END FUNCTION lammps_extract_variable
!INTEGER (c_int) lammps_set_variable !INTEGER (c_int) lammps_set_variable
@ -647,7 +701,7 @@ CONTAINS
! the assignment is actually overloaded so as to bind the pointers to ! the assignment is actually overloaded so as to bind the pointers to
! lammps data based on the information available from LAMMPS ! lammps data based on the information available from LAMMPS
FUNCTION lmp_extract_global(self, name) RESULT (global_data) FUNCTION lmp_extract_global(self, name) RESULT (global_data)
CLASS(lammps), INTENT(IN) :: self CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: name CHARACTER(LEN=*), INTENT(IN) :: name
TYPE(lammps_data) :: global_data TYPE(lammps_data) :: global_data
@ -674,6 +728,7 @@ CONTAINS
Cptr = lammps_extract_global(self%handle, Cname) Cptr = lammps_extract_global(self%handle, Cname)
CALL lammps_free(Cname) CALL lammps_free(Cname)
global_data%lammps_instance => self
SELECT CASE (datatype) SELECT CASE (datatype)
CASE (LAMMPS_INT) CASE (LAMMPS_INT)
IF ( length == 1 ) THEN IF ( length == 1 ) THEN
@ -704,7 +759,7 @@ CONTAINS
length = c_strlen(Cptr) length = c_strlen(Cptr)
CALL C_F_POINTER(Cptr, Fptr, [length]) CALL C_F_POINTER(Cptr, Fptr, [length])
ALLOCATE ( CHARACTER(LEN=length) :: global_data%str ) ALLOCATE ( CHARACTER(LEN=length) :: global_data%str )
FORALL ( I=1:length ) FORALL ( i=1:length )
global_data%str(i:i) = Fptr(i) global_data%str(i:i) = Fptr(i)
END FORALL END FORALL
CASE DEFAULT CASE DEFAULT
@ -717,7 +772,7 @@ CONTAINS
! the assignment is actually overloaded so as to bind the pointers to ! the assignment is actually overloaded so as to bind the pointers to
! lammps data based on the information available from LAMMPS ! lammps data based on the information available from LAMMPS
FUNCTION lmp_extract_atom (self, name) RESULT (peratom_data) FUNCTION lmp_extract_atom (self, name) RESULT (peratom_data)
CLASS(lammps), INTENT(IN) :: self CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: name CHARACTER(LEN=*), INTENT(IN) :: name
TYPE(lammps_data) :: peratom_data TYPE(lammps_data) :: peratom_data
@ -748,6 +803,7 @@ CONTAINS
nrows = 1 nrows = 1
END SELECT END SELECT
peratom_data%lammps_instance => self
SELECT CASE (datatype) SELECT CASE (datatype)
CASE (LAMMPS_INT) CASE (LAMMPS_INT)
peratom_data%datatype = DATA_INT_1D peratom_data%datatype = DATA_INT_1D
@ -772,16 +828,10 @@ CONTAINS
CASE (-1) CASE (-1)
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'per-atom property ' // name // 'not found in extract_setting') 'per-atom property ' // name // 'not found in extract_setting')
! WRITE(ERROR_UNIT,'(A)') 'ERROR: per-atom property "' // name // &
! '" not found.'
! STOP 2
CASE DEFAULT CASE DEFAULT
WRITE(error_msg,'(A,I0,A)') 'return value ', datatype, & WRITE(error_msg,'(A,I0,A)') 'return value ', datatype, &
' from lammps_extract_atom_datatype not known [Fortran/extract_atom]' ' from lammps_extract_atom_datatype not known [Fortran/extract_atom]'
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg)
! WRITE(ERROR_UNIT,'(A,I0,A)') 'ERROR: return value ', datatype, &
! ' from lammps_extract_atom_datatype not known'
! STOP 1
END SELECT END SELECT
END FUNCTION lmp_extract_atom END FUNCTION lmp_extract_atom
@ -789,12 +839,11 @@ CONTAINS
! the assignment operator is overloaded so as to bind the pointers to ! the assignment operator is overloaded so as to bind the pointers to
! lammps data based on the information available from LAMMPS ! lammps data based on the information available from LAMMPS
FUNCTION lmp_extract_compute (self, id, style, type) RESULT (compute_data) FUNCTION lmp_extract_compute (self, id, style, type) RESULT (compute_data)
CLASS(lammps), INTENT(IN) :: self CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: id CHARACTER(LEN=*), INTENT(IN) :: id
INTEGER(c_int), INTENT(IN) :: style, type INTEGER(c_int), INTENT(IN) :: style, type
TYPE(lammps_data) :: compute_data TYPE(lammps_data) :: compute_data
INTEGER(c_int) :: datatype
TYPE(c_ptr) :: Cid, Cptr, Ctemp TYPE(c_ptr) :: Cid, Cptr, Ctemp
INTEGER :: nrows, ncols, length INTEGER :: nrows, ncols, length
INTEGER(c_int), POINTER :: temp INTEGER(c_int), POINTER :: temp
@ -809,6 +858,7 @@ CONTAINS
END IF END IF
! Remember that rows and columns in C are transposed in Fortran! ! Remember that rows and columns in C are transposed in Fortran!
compute_data%lammps_instance => self
SELECT CASE (type) SELECT CASE (type)
CASE (LMP_TYPE_SCALAR) CASE (LMP_TYPE_SCALAR)
compute_data%datatype = DATA_DOUBLE compute_data%datatype = DATA_DOUBLE
@ -847,14 +897,161 @@ CONTAINS
CALL C_F_POINTER(Ccomputeptr(1), compute_data%r64_mat, [nrows, ncols]) CALL C_F_POINTER(Ccomputeptr(1), compute_data%r64_mat, [nrows, ncols])
CASE DEFAULT CASE DEFAULT
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'unknown type value passed to extract_compute') 'unknown type value passed to extract_compute [Fortran API]')
!WRITE(ERROR_UNIT,'(A,I0,A)') 'ERROR: unknown type value ', type, &
! 'passed to extract_compute'
!STOP 1
END SELECT END SELECT
CALL lammps_free(Cid) CALL lammps_free(Cid)
END FUNCTION lmp_extract_compute END FUNCTION lmp_extract_compute
FUNCTION lmp_extract_fix(self, id, style, type, nrow, ncol) RESULT (fix_data)
CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: id
INTEGER(c_int), INTENT(IN) :: style, type
INTEGER(c_int), INTENT(IN), OPTIONAL :: nrow, ncol
TYPE(lammps_fix_data) :: fix_data
TYPE(c_ptr) :: Cid, Cptr, Ctemp
TYPE(c_ptr), DIMENSION(:), POINTER :: Cfixptr
INTEGER(c_int) :: Cnrow, Cncol
REAL(c_double), POINTER :: Fptr
INTEGER :: nrows, ncols
INTEGER(c_int), POINTER :: temp
! We transpose ncol and nrow so the array appears to be transposed for
! global data, as it would be if we could access the C++ array directly
Cnrow = -1
Cncol = -1
IF ( PRESENT(nrow) ) THEN
IF ( .NOT. PRESENT(ncol) ) THEN
! Presumably the argument that's there is the vector length
Cnrow = nrow - 1_c_int
Cncol = -1_c_int
ELSE
! Otherwise, the array is transposed, so...reverse the indices
Cncol = nrow - 1_c_int
END IF
END IF
IF ( PRESENT(ncol) ) Cnrow = ncol - 1_c_int
Cid = f2c_string(id)
Cptr = lammps_extract_fix(self%handle, Cid, style, type, Cnrow, Cncol)
IF ( .NOT. C_ASSOCIATED(Cptr) ) THEN
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'Pointer from LAMMPS is NULL for fix id "' // id &
// '" [Fortran/extract_fix]')
END IF
fix_data%lammps_instance => self
SELECT CASE (style)
CASE (LMP_STYLE_GLOBAL)
fix_data%datatype = DATA_DOUBLE
CALL C_F_POINTER(Cptr, Fptr)
fix_data%r64 = Fptr
CALL lammps_free(Cptr)
CASE (LMP_STYLE_ATOM, LMP_STYLE_LOCAL)
SELECT CASE (type)
CASE (LMP_TYPE_SCALAR)
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'There is no such thing as a per-atom or local scalar&
& [Fortran/extract_fix]')
CASE (LMP_TYPE_VECTOR)
fix_data%datatype = DATA_DOUBLE_1D
IF ( STYLE == LMP_STYLE_ATOM ) THEN
nrows = self%extract_setting('nmax')
ELSE
Ctemp = lammps_extract_fix(self%handle, Cid, style, &
LMP_SIZE_VECTOR, 0_c_int,0_c_int)
CALL C_F_POINTER(Ctemp, temp)
nrows = temp
END IF
CALL C_F_POINTER(Cptr, fix_data%r64_vec, [nrows])
CASE (LMP_TYPE_ARRAY)
fix_data%datatype = DATA_DOUBLE_2D
IF ( STYLE == LMP_STYLE_ATOM ) THEN
! Fortran array is transposed relative to C
ncols = self%extract_setting('nmax')
Ctemp = lammps_extract_fix(self%handle, Cid, style, &
LMP_SIZE_COLS, 0_c_int,0_c_int)
CALL C_F_POINTER(Ctemp, temp)
nrows = temp
ELSE
! Fortran array is transposed relative to C
Ctemp = lammps_extract_fix(self%handle, Cid, style, &
LMP_SIZE_COLS, 0_c_int,0_c_int)
CALL C_F_POINTER(Ctemp, temp)
nrows = temp
Ctemp = lammps_extract_fix(self%handle, Cid, style, &
LMP_SIZE_ROWS, 0_c_int,0_c_int)
CALL C_F_POINTER(Ctemp, temp)
ncols = temp
END IF
! First, we dereference the void** to point to a void* pointer
CALL C_F_POINTER(Cptr, Cfixptr, [ncols])
! Cfixptr(1) now points to the first element of the array
CALL C_F_POINTER(Cfixptr(1), fix_data%r64_mat, [nrows, ncols])
CASE DEFAULT
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'unknown type value passed to extract_fix [Fortran API]')
END SELECT
CASE DEFAULT
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'unknown style value passed to extract_fix [Fortran API]')
END SELECT
CALL lammps_free(Cid)
END FUNCTION lmp_extract_fix
! equivalent function to lammps_extract_variable
FUNCTION lmp_extract_variable(self, name, group) RESULT (variable_data)
CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: name
CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: group
TYPE(lammps_variable_data) :: variable_data
TYPE(c_ptr) :: Cptr, Cname, Cgroup
INTEGER :: length, i
CHARACTER(KIND=c_char, LEN=1), DIMENSION(:), POINTER :: Cstring
INTEGER(c_int) :: datatype
REAL(c_double), POINTER :: double
REAL(c_double), DIMENSION(:), POINTER :: double_vec
Cname = f2c_string(name)
IF ( PRESENT(group) ) THEN
Cgroup = f2c_string(group)
ELSE
Cgroup = c_null_ptr
END IF
datatype = lammps_extract_variable_datatype(self%handle, Cname)
Cptr = lammps_extract_variable(self%handle, Cname, Cgroup)
CALL lammps_free(Cname)
CALL lammps_free(Cgroup)
SELECT CASE (datatype)
CASE (LMP_VAR_EQUAL)
variable_data%datatype = DATA_DOUBLE
CALL C_F_POINTER(Cptr, double)
variable_data%r64 = double
CALL lammps_free(Cptr)
CASE (LMP_VAR_ATOM)
variable_data%datatype = DATA_DOUBLE_1D
length = lmp_extract_setting(self, 'nlocal')
CALL C_F_POINTER(Cptr, double_vec, [length])
variable_data%r64_vec = double_vec
CALL lammps_free(Cptr)
CASE (LMP_VAR_STRING)
variable_data%datatype = DATA_STRING
length = c_strlen(Cptr)
CALL C_F_POINTER(Cptr, Cstring, [length])
ALLOCATE ( CHARACTER(LEN=length) :: variable_data%str )
FORALL ( i=1:length )
variable_data%str(i:i) = Cstring(i)
END FORALL
CASE DEFAULT
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'Unknown variable type returned from &
&lammps_extract_variable_datatype [Fortran/extract_variable]')
END SELECT
END FUNCTION lmp_extract_variable
! equivalent function to lammps_version() ! equivalent function to lammps_version()
INTEGER FUNCTION lmp_version(self) INTEGER FUNCTION lmp_version(self)
CLASS(lammps), INTENT(IN) :: self CLASS(lammps), INTENT(IN) :: self
@ -873,7 +1070,7 @@ CONTAINS
SUBROUTINE lmp_flush_buffers(self) SUBROUTINE lmp_flush_buffers(self)
CLASS(lammps), INTENT(IN) :: self CLASS(lammps), INTENT(IN) :: self
call lammps_flush_buffers(self%handle) CALL lammps_flush_buffers(self%handle)
END SUBROUTINE lmp_flush_buffers END SUBROUTINE lmp_flush_buffers
! equivalent function to lammps_has_error ! equivalent function to lammps_has_error
@ -891,14 +1088,16 @@ CONTAINS
CHARACTER(LEN=*), INTENT(OUT) :: buffer CHARACTER(LEN=*), INTENT(OUT) :: buffer
INTEGER, INTENT(OUT), OPTIONAL :: status INTEGER, INTENT(OUT), OPTIONAL :: status
INTEGER(c_int) :: length, Cstatus, i INTEGER(c_int) :: length, Cstatus, i
TYPE(c_ptr) :: Cbuffer TYPE(c_ptr) :: Cptr
CHARACTER(KIND=c_char, LEN=1), DIMENSION(:), POINTER :: Cbuffer
buffer = '' buffer = ''
IF ( lmp_has_error(self) ) THEN IF ( lmp_has_error(self) ) THEN
length = LEN(buffer) length = LEN(buffer)
Cbuffer = f2cstring(buffer) Cptr = f2c_string(buffer)
Cstatus = lammps_get_last_error_message(self%handle, Cbuffer, length) Cstatus = lammps_get_last_error_message(self%handle, Cptr, length)
length = MIN(LEN(buffer), c_strlen(Cbuffer)) length = MIN(LEN(buffer), c_strlen(Cptr))
CALL C_F_POINTER(Cptr, Cbuffer, [length])
FORALL ( i=1:length ) FORALL ( i=1:length )
buffer(i:i) = Cbuffer(i) buffer(i:i) = Cbuffer(i)
END FORALL END FORALL
@ -923,7 +1122,7 @@ CONTAINS
IF ( rhs%datatype == DATA_INT ) THEN IF ( rhs%datatype == DATA_INT ) THEN
lhs => rhs%i32 lhs => rhs%i32
ELSE ELSE
CALL assignment_error(rhs%datatype, 'scalar int') CALL assignment_error(rhs, 'scalar int')
END IF END IF
END SUBROUTINE assign_int_to_lammps_data END SUBROUTINE assign_int_to_lammps_data
@ -934,7 +1133,7 @@ CONTAINS
IF ( rhs%datatype == DATA_INT64 ) THEN IF ( rhs%datatype == DATA_INT64 ) THEN
lhs => rhs%i64 lhs => rhs%i64
ELSE ELSE
CALL assignment_error(rhs%datatype, 'scalar long int') CALL assignment_error(rhs, 'scalar long int')
END IF END IF
END SUBROUTINE assign_int64_to_lammps_data END SUBROUTINE assign_int64_to_lammps_data
@ -945,7 +1144,7 @@ CONTAINS
IF ( rhs%datatype == DATA_INT_1D ) THEN IF ( rhs%datatype == DATA_INT_1D ) THEN
lhs => rhs%i32_vec lhs => rhs%i32_vec
ELSE ELSE
CALL assignment_error(rhs%datatype, 'vector of ints') CALL assignment_error(rhs, 'vector of ints')
END IF END IF
END SUBROUTINE assign_intvec_to_lammps_data END SUBROUTINE assign_intvec_to_lammps_data
@ -956,7 +1155,7 @@ CONTAINS
IF ( rhs%datatype == DATA_INT64_1D ) THEN IF ( rhs%datatype == DATA_INT64_1D ) THEN
lhs => rhs%i64_vec lhs => rhs%i64_vec
ELSE ELSE
CALL assignment_error(rhs%datatype, 'vector of long ints') CALL assignment_error(rhs, 'vector of long ints')
END IF END IF
END SUBROUTINE assign_int64vec_to_lammps_data END SUBROUTINE assign_int64vec_to_lammps_data
@ -967,7 +1166,7 @@ CONTAINS
IF ( rhs%datatype == DATA_DOUBLE ) THEN IF ( rhs%datatype == DATA_DOUBLE ) THEN
lhs => rhs%r64 lhs => rhs%r64
ELSE ELSE
CALL assignment_error(rhs%datatype, 'scalar double') CALL assignment_error(rhs, 'scalar double')
END IF END IF
END SUBROUTINE assign_double_to_lammps_data END SUBROUTINE assign_double_to_lammps_data
@ -978,7 +1177,7 @@ CONTAINS
IF ( rhs%datatype == DATA_DOUBLE_1D ) THEN IF ( rhs%datatype == DATA_DOUBLE_1D ) THEN
lhs => rhs%r64_vec lhs => rhs%r64_vec
ELSE ELSE
CALL assignment_error(rhs%datatype, 'vector of doubles') CALL assignment_error(rhs, 'vector of doubles')
END IF END IF
END SUBROUTINE assign_doublevec_to_lammps_data END SUBROUTINE assign_doublevec_to_lammps_data
@ -989,7 +1188,7 @@ CONTAINS
IF ( rhs%datatype == DATA_DOUBLE_2D ) THEN IF ( rhs%datatype == DATA_DOUBLE_2D ) THEN
lhs => rhs%r64_mat lhs => rhs%r64_mat
ELSE ELSE
CALL assignment_error(rhs%datatype, 'matrix of doubles') CALL assignment_error(rhs, 'matrix of doubles')
END IF END IF
END SUBROUTINE assign_doublemat_to_lammps_data END SUBROUTINE assign_doublemat_to_lammps_data
@ -1000,17 +1199,81 @@ CONTAINS
IF ( rhs%datatype == DATA_STRING ) THEN IF ( rhs%datatype == DATA_STRING ) THEN
lhs = rhs%str lhs = rhs%str
ELSE ELSE
CALL assignment_error(rhs%datatype, 'string') CALL assignment_error(rhs, 'string')
END IF END IF
END SUBROUTINE assign_string_to_lammps_data END SUBROUTINE assign_string_to_lammps_data
SUBROUTINE assignment_error (type1, type2) ! ----------------------------------------------------------------------
INTEGER (c_int) :: type1 ! functions to assign user-space pointers to LAMMPS *fix* data
CHARACTER (LEN=*) :: type2 ! ----------------------------------------------------------------------
INTEGER, PARAMETER :: ERROR_CODE = 1 SUBROUTINE assign_double_to_lammps_fix_data (lhs, rhs)
REAL(c_double), INTENT(OUT) :: lhs
CLASS(lammps_fix_data), INTENT(IN) :: rhs
IF ( rhs%datatype == DATA_DOUBLE ) THEN
lhs = rhs%r64
ELSE
CALL assignment_error(rhs, 'scalar double')
END IF
END SUBROUTINE assign_double_to_lammps_fix_data
SUBROUTINE assign_doublevec_to_lammps_fix_data (lhs, rhs)
REAL(c_double), DIMENSION(:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_fix_data), INTENT(IN) :: rhs
IF ( rhs%datatype == DATA_DOUBLE_1D ) THEN
lhs => rhs%r64_vec
ELSE
CALL assignment_error(rhs, 'vector of doubles')
END IF
END SUBROUTINE assign_doublevec_to_lammps_fix_data
SUBROUTINE assign_doublemat_to_lammps_fix_data (lhs, rhs)
REAL(c_double), DIMENSION(:,:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_fix_data), INTENT(IN) :: rhs
IF ( rhs%datatype == DATA_DOUBLE_2D ) THEN
lhs => rhs%r64_mat
ELSE
CALL assignment_error(rhs, 'matrix of doubles')
END IF
END SUBROUTINE assign_doublemat_to_lammps_fix_data
! ----------------------------------------------------------------------
! functions to assign user-space pointers to LAMMPS *variable* data
! ----------------------------------------------------------------------
SUBROUTINE assign_double_to_lammps_variable_data (lhs, rhs)
REAL(c_double), INTENT(OUT) :: lhs
CLASS(lammps_variable_data), INTENT(IN) :: rhs
IF ( rhs%datatype == DATA_DOUBLE ) THEN
lhs = rhs%r64
ELSE
CALL assignment_error(rhs, 'scalar double')
END IF
END SUBROUTINE assign_double_to_lammps_variable_data
SUBROUTINE assign_doublevec_to_lammps_variable_data (lhs, rhs)
REAL(c_double), DIMENSION(:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_variable_data), INTENT(IN) :: rhs
IF ( rhs%datatype == DATA_DOUBLE_1D ) THEN
lhs = rhs%r64_vec
ELSE
CALL assignment_error(rhs, 'vector of doubles')
END IF
END SUBROUTINE assign_doublevec_to_lammps_variable_data
! ----------------------------------------------------------------------
! Generic function to catch all errors in assignments of LAMMPS data to
! user-space variables/pointers
! ----------------------------------------------------------------------
SUBROUTINE assignment_error (type1, str2)
CLASS(lammps_data_baseclass), INTENT(IN) :: type1
CHARACTER (LEN=*), INTENT(IN) :: str2
CHARACTER (LEN=:), ALLOCATABLE :: str1 CHARACTER (LEN=:), ALLOCATABLE :: str1
SELECT CASE (type1) SELECT CASE (type1%datatype)
CASE (DATA_INT) CASE (DATA_INT)
str1 = 'scalar int' str1 = 'scalar int'
CASE (DATA_INT_1D) CASE (DATA_INT_1D)
@ -1032,11 +1295,8 @@ CONTAINS
CASE DEFAULT CASE DEFAULT
str1 = 'that type' str1 = 'that type'
END SELECT END SELECT
!CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, 'cannot associate ' & CALL lmp_error(type1%lammps_instance, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
! // str1 // ' with ' // type2 // ' [Fortran API]') 'cannot associate ' // str1 // ' with ' // str2 // ' [Fortran API]')
WRITE (ERROR_UNIT,'(A)') 'ERROR (Fortran API): cannot associate ' &
// str1 // ' with ' // type2
STOP ERROR_CODE
END SUBROUTINE assignment_error END SUBROUTINE assignment_error
! ---------------------------------------------------------------------- ! ----------------------------------------------------------------------

1
python/lammps/constants.py
View File

@ -42,6 +42,7 @@ LMP_ERROR_UNIVERSE = 8
LMP_VAR_EQUAL = 0 LMP_VAR_EQUAL = 0
LMP_VAR_ATOM = 1 LMP_VAR_ATOM = 1
LMP_VAR_STRING = 2
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------

41
src/library.cpp
View File

@ -2130,6 +2130,47 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
/** Get data type of a LAMMPS variable
*
\verbatim embed:rst
This function returns an integer that encodes the data type of the variable
with the specified name. See :cpp:enum:`_LMP_VAR_CONST` for valid values.
Callers of :cpp:func:`lammps_extract_variable` can use this information to
decide how to cast the (void*) pointer and access the data.
..versionadded:: TBD
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param name string with the name of the extracted variable
* \return integer constant encoding the data type of the property
* or -1 if not found.
**/
int lammps_extract_variable_datatype(void *handle, const char *name)
{
auto lmp = (LAMMPS*) handle;
BEGIN_CAPTURE
{
int ivar = lmp->input->variable->find(name);
if ( ivar < 0 ) return -1;
if (lmp->input->variable->equalstyle(ivar))
return LMP_VAR_EQUAL;
else if (lmp->input->variable->atomstyle(ivar))
return LMP_VAR_ATOM;
else
return LMP_VAR_STRING;
}
END_CAPTURE
return -1;
}
/* ---------------------------------------------------------------------- */
/** Set the value of a string-style variable. /** Set the value of a string-style variable.
* *
* This function assigns a new value from the string str to the * This function assigns a new value from the string str to the

24
src/library.h
View File

@ -40,7 +40,8 @@
/** Data type constants for extracting data from atoms, computes and fixes /** Data type constants for extracting data from atoms, computes and fixes
* *
* Must be kept in sync with the equivalent constants in lammps/constants.py */ * Must be kept in sync with the equivalent constants in lammps/constants.py
* and fortran/lammps.f90 */
enum _LMP_DATATYPE_CONST { enum _LMP_DATATYPE_CONST {
LAMMPS_INT = 0, /*!< 32-bit integer (array) */ LAMMPS_INT = 0, /*!< 32-bit integer (array) */
@ -54,7 +55,8 @@ enum _LMP_DATATYPE_CONST {
/** Style constants for extracting data from computes and fixes. /** Style constants for extracting data from computes and fixes.
* *
* Must be kept in sync with the equivalent constants in lammps/constants.py */ * Must be kept in sync with the equivalent constants in lammps/constants.py
* and fortran/lammps.f90 */
enum _LMP_STYLE_CONST { enum _LMP_STYLE_CONST {
LMP_STYLE_GLOBAL = 0, /*!< return global data */ LMP_STYLE_GLOBAL = 0, /*!< return global data */
@ -64,7 +66,8 @@ enum _LMP_STYLE_CONST {
/** Type and size constants for extracting data from computes and fixes. /** Type and size constants for extracting data from computes and fixes.
* *
* Must be kept in sync with the equivalent constants in lammps/constants.py */ * Must be kept in sync with the equivalent constants in lammps/constants.py
* and fortran/lammps.f90 */
enum _LMP_TYPE_CONST { enum _LMP_TYPE_CONST {
LMP_TYPE_SCALAR = 0, /*!< return scalar */ LMP_TYPE_SCALAR = 0, /*!< return scalar */
@ -77,7 +80,8 @@ enum _LMP_TYPE_CONST {
/** Error codes to select the suitable function in the Error class /** Error codes to select the suitable function in the Error class
* *
* Must be kept in sync with the equivalent constants in lammps/constants.py */ * Must be kept in sync with the equivalent constants in lammps/constants.py
* and fortran/lammps.f90 */
enum _LMP_ERROR_CONST { enum _LMP_ERROR_CONST {
LMP_ERROR_WARNING = 0, /*!< call Error::warning() */ LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
@ -87,6 +91,17 @@ enum _LMP_ERROR_CONST {
LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */ LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */
}; };
/** Variable style constants for extracting data from variables
*
* Must be kept in sync with the equivalent constants in lammps/constants.py
* and fortran/lammps.f90 */
enum _LMP_VAR_CONST {
LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */
LMP_VAR_STRING = 2 /*!< return value will be a string (catch-all) */
};
/* Ifdefs to allow this file to be included in C and C++ programs */ /* Ifdefs to allow this file to be included in C and C++ programs */
#ifdef __cplusplus #ifdef __cplusplus
@ -153,6 +168,7 @@ void *lammps_extract_atom(void *handle, const char *name);
void *lammps_extract_compute(void *handle, const char *, int, int); void *lammps_extract_compute(void *handle, const char *, int, int);
void *lammps_extract_fix(void *handle, const char *, int, int, int, int); void *lammps_extract_fix(void *handle, const char *, int, int, int, int);
void *lammps_extract_variable(void *handle, const char *, const char *); void *lammps_extract_variable(void *handle, const char *, const char *);
int lammps_extract_variable_datatype(void *handle, const char *name);
int lammps_set_variable(void *, char *, char *); int lammps_set_variable(void *, char *, char *);
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

4
unittest/fortran/CMakeLists.txt
View File

@ -65,6 +65,10 @@ if(CMAKE_Fortran_COMPILER)
target_link_libraries(test_fortran_extract_compute PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) target_link_libraries(test_fortran_extract_compute PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractCompute COMMAND test_fortran_extract_compute) add_test(NAME FortranExtractCompute COMMAND test_fortran_extract_compute)
add_executable(test_fortran_extract_fix wrap_extract_fix.cpp test_fortran_extract_fix.f90)
target_link_libraries(test_fortran_extract_fix PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractFix COMMAND test_fortran_extract_fix)
else() else()
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran compiler") message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran compiler")
endif() endif()

118
unittest/fortran/test_fortran_extract_fix.f90 Normal file
View File

@ -0,0 +1,118 @@
MODULE keepfix
USE liblammps
TYPE(LAMMPS) :: lmp
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: demo_input = &
[ CHARACTER(LEN=40) :: &
'region box block 0 $x 0 3 0 4', &
'create_box 1 box', &
'create_atoms 1 single 1.0 1.0 ${zpos}' ]
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: cont_input = &
[ CHARACTER(LEN=40) :: &
'create_atoms 1 single &', &
' 0.2 0.1 0.1', &
'create_atoms 1 single 0.5 0.5 0.5' ]
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: pair_input = &
[ CHARACTER(LEN=40) :: &
'pair_style lj/cut 2.5', &
'pair_coeff 1 1 1.0 1.0', &
'mass 1 2.0' ]
END MODULE keepfix
FUNCTION f_lammps_with_args() BIND(C)
USE ISO_C_BINDING, ONLY: C_ptr
USE liblammps
USE keepfix, ONLY: lmp
IMPLICIT NONE
TYPE(C_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
[ CHARACTER(len=12) :: 'liblammps', '-log', 'none', &
'-echo','screen','-nocite','-var','zpos','1.5','-var','x','2']
lmp = lammps(args)
f_lammps_with_args = lmp%handle
END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepfix, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
lmp%handle = C_NULL_PTR
END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_fix () BIND(C)
USE LIBLAMMPS
USE keepfix, ONLY : lmp, demo_input, cont_input, pair_input
IMPLICIT NONE
CALL lmp%commands_list(demo_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command("fix state all store/state 0 z") ! per-atom vector
CALL lmp%command("fix move all move linear 0 0 0") ! for per-atom array
CALL lmp%command("fix recenter all recenter 1 1 1") ! global scalar, vector
CALL lmp%command("variable natoms equal count(all)")
CALL lmp%command("variable ts equal step")
CALL lmp%command("fix vec all vector 1 v_natoms v_ts") ! global array
CALL lmp%command("run 1") ! must be 1, otherwise move/recenter won't happen
END SUBROUTINE f_lammps_setup_extract_fix
FUNCTION f_lammps_extract_fix_global_scalar () BIND(C) RESULT(scalar)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
USE LIBLAMMPS
USE keepfix, ONLY : lmp
IMPLICIT NONE
REAL(C_double) :: scalar
scalar = lmp%extract_fix("recenter", lmp%style%global, lmp%type%scalar)
END FUNCTION f_lammps_extract_fix_global_scalar
FUNCTION f_lammps_extract_fix_global_vector (i) BIND(C) RESULT(element)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double) :: element
element = lmp%extract_fix("recenter", lmp%style%global, lmp%type%vector, i)
END FUNCTION f_lammps_extract_fix_global_vector
FUNCTION f_lammps_extract_fix_global_array (i,j) BIND(C) RESULT(element)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i, j
REAL(C_double) :: element
element = lmp%extract_fix("vec", lmp%style%global, lmp%type%array, i, j)
END FUNCTION f_lammps_extract_fix_global_array
FUNCTION f_lammps_extract_fix_peratom_vector (i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double) :: f_lammps_extract_fix_peratom_vector
REAL(C_double), DIMENSION(:), POINTER :: vector
vector = lmp%extract_fix("state", lmp%style%atom, lmp%type%vector, -1, -1)
f_lammps_extract_fix_peratom_vector = vector(i)
END FUNCTION f_lammps_extract_fix_peratom_vector
FUNCTION f_lammps_extract_fix_peratom_array (i,j) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i, j
REAL(C_double) :: f_lammps_extract_fix_peratom_array
REAL(C_double), DIMENSION(:,:), POINTER :: array
array = lmp%extract_fix("move", lmp%style%atom, lmp%type%array, -1, -1)
f_lammps_extract_fix_peratom_array = array(i,j)
END FUNCTION f_lammps_extract_fix_peratom_array

107
unittest/fortran/wrap_extract_fix.cpp Normal file
View File

@ -0,0 +1,107 @@
// unit tests for extracting compute data from a LAMMPS instance through the
// Fortran wrapper
#include <cstdio>
#include "lammps.h"
#include "library.h"
#include <mpi.h>
#include <string>
#include <cstdlib>
#include <cstdint>
#include "gtest/gtest.h"
// prototypes for Fortran reverse wrapper functions
extern "C" {
void *f_lammps_with_args();
void f_lammps_close();
void f_lammps_setup_extract_fix();
double f_lammps_extract_fix_global_scalar();
double f_lammps_extract_fix_global_vector(int);
double f_lammps_extract_fix_global_array(int,int);
double f_lammps_extract_fix_peratom_vector(int);
double f_lammps_extract_fix_peratom_array(int,int);
double f_lammps_extract_fix_local_vector(int);
double f_lammps_extract_fix_local_array(int,int);
}
class LAMMPS_extract_fix : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_extract_fix() = default;
~LAMMPS_extract_fix() override = default;
void SetUp() override
{
::testing::internal::CaptureStdout();
lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
f_lammps_close();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:");
lmp = nullptr;
}
};
TEST_F(LAMMPS_extract_fix, global_scalar)
{
f_lammps_setup_extract_fix();
double *scalar = (double*) lammps_extract_fix(lmp, "recenter",
LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR, -1, -1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_scalar(), *scalar);
lammps_free(scalar);
};
TEST_F(LAMMPS_extract_fix, global_vector)
{
f_lammps_setup_extract_fix();
double *x = (double*) lammps_extract_fix(lmp, "recenter",
LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, -1);
double *y = (double*) lammps_extract_fix(lmp, "recenter",
LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 1, -1);
double *z = (double*) lammps_extract_fix(lmp, "recenter",
LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 2, -1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_vector(1), *x);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_vector(2), *y);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_vector(3), *z);
lammps_free(x);
lammps_free(y);
lammps_free(z);
};
TEST_F(LAMMPS_extract_fix, global_array)
{
f_lammps_setup_extract_fix();
double natoms = lammps_get_natoms(lmp);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(1,1), natoms);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(1,2), natoms);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(2,1), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_global_array(2,2), 1.0);
};
TEST_F(LAMMPS_extract_fix, peratom_vector)
{
f_lammps_setup_extract_fix();
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_vector(1), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_vector(2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_vector(3), 0.5);
};
TEST_F(LAMMPS_extract_fix, peratom_array)
{
f_lammps_setup_extract_fix();
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(1,1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(2,1), 1.0);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(3,1), 1.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(1,2), 0.2);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(2,2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(3,2), 0.1);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(1,3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(2,3), 0.5);
EXPECT_DOUBLE_EQ(f_lammps_extract_fix_peratom_array(3,3), 0.5);
};