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spell check; updated false positives; whitespace

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This commit is contained in:
Karl Hammond
2022-09-30 18:50:16 -05:00
parent d301ff9961
commit 953c3d0cad
3 changed files with 96 additions and 93 deletions
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2
doc/src/Fortran.rst
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@ -986,7 +986,7 @@ Procedures Bound to the lammps Derived Type
The pointers returned by this function for per-atom or local data are
generally not persistent, since the computed data may be redistributed,
reallocated, and reordered at every invocation of the fix. It is thus
advisable to reinvoke this function before the data are accessed or to
advisable to re-invoke this function before the data are accessed or to
make a copy if the data are to be used after other LAMMPS commands have
been issued.

3
doc/utils/sphinx-config/false_positives.txt
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@ -78,6 +78,7 @@ Alexey
ali
aliceblue
Allinger
allocatable
allocator
allocators
allosws
@ -657,6 +658,7 @@ Dcut
de
dE
De
deallocate
deallocated
debye
Debye
@ -691,6 +693,7 @@ dequidt
Dequidt
der
dereference
dereferenced
derekt
Deresiewicz
Derjagin

152
fortran/lammps.f90
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@ -43,7 +43,7 @@ MODULE LIBLAMMPS
! src/library.h and python/lammps/constants.py
!
! These are NOT part of the API (the part the user sees)
INTEGER (c_int), PARAMETER :: &
INTEGER(c_int), PARAMETER :: &
LAMMPS_INT = 0, & ! 32-bit integer (array)
LAMMPS_INT_2D = 1, & ! two-dimensional 32-bit integer array
LAMMPS_DOUBLE = 2, & ! 64-bit double (array)
@ -329,7 +329,7 @@ MODULE LIBLAMMPS
INTEGER(c_int) :: lammps_extract_global_datatype
END FUNCTION lammps_extract_global_datatype
FUNCTION c_strlen (str) BIND(C,name='strlen')
FUNCTION c_strlen(str) BIND(C,name='strlen')
IMPORT :: c_ptr, c_size_t
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: str
@ -387,11 +387,11 @@ MODULE LIBLAMMPS
TYPE(c_ptr) :: lammps_extract_variable
END FUNCTION lammps_extract_variable
FUNCTION lammps_set_variable (handle, name, str) BIND(C)
FUNCTION lammps_set_variable(handle, name, str) BIND(C)
IMPORT :: c_int, c_ptr
IMPLICIT NONE
TYPE (c_ptr), VALUE :: handle, name, str
INTEGER (c_int) :: lammps_set_variable
TYPE(c_ptr), VALUE :: handle, name, str
INTEGER(c_int) :: lammps_set_variable
END FUNCTION lammps_set_variable
!SUBROUTINE lammps_gather_atoms
@ -415,15 +415,15 @@ MODULE LIBLAMMPS
!SUBROUTINE lammps_scatter_subset
!(generic / id, type, and image are special) / requires LAMMPS_BIGBIG
!INTEGER (C_int) FUNCTION lammps_create_atoms
!INTEGER(c_int) FUNCTION lammps_create_atoms
!INTEGER (C_int) FUNCTION lammps_find_pair_neighlist
!INTEGER(c_int) FUNCTION lammps_find_pair_neighlist
!INTEGER (C_int) FUNCTION lammps_find_fix_neighlist
!INTEGER(c_int) FUNCTION lammps_find_fix_neighlist
!INTEGER (C_int) FUNCTION lammps_find_compute_neighlist
!INTEGER(c_int) FUNCTION lammps_find_compute_neighlist
!INTEGER (C_int) FUNCTION lammps_neighlist_num_elements
!INTEGER(c_int) FUNCTION lammps_neighlist_num_elements
!SUBROUTINE lammps_neighlist_element_neighbors
@ -434,11 +434,11 @@ MODULE LIBLAMMPS
INTEGER(c_int) :: lammps_version
END FUNCTION lammps_version
SUBROUTINE lammps_get_os_info (buffer, buf_size) BIND(C)
SUBROUTINE lammps_get_os_info(buffer, buf_size) BIND(C)
IMPORT :: C_ptr, C_int
IMPLICIT NONE
TYPE (C_ptr), VALUE :: buffer
INTEGER (C_int), VALUE :: buf_size
TYPE(C_ptr), VALUE :: buffer
INTEGER(C_int), VALUE :: buf_size
END SUBROUTINE lammps_get_os_info
FUNCTION lammps_config_has_mpi_support() BIND(C)
@ -474,28 +474,28 @@ MODULE LIBLAMMPS
FUNCTION lammps_config_has_exceptions() BIND(C)
IMPORT :: c_int
IMPLICIT NONE
INTEGER (c_int) :: lammps_config_has_exceptions
INTEGER(c_int) :: lammps_config_has_exceptions
END FUNCTION lammps_config_has_exceptions
FUNCTION lammps_config_has_package(name) BIND(C)
IMPORT :: C_int, C_ptr
IMPLICIT NONE
TYPE (C_ptr), VALUE :: name
INTEGER (c_int) :: lammps_config_has_package
TYPE(C_ptr), VALUE :: name
INTEGER(c_int) :: lammps_config_has_package
END FUNCTION lammps_config_has_package
FUNCTION lammps_config_package_count() BIND(C)
IMPORT :: C_int
IMPLICIT NONE
INTEGER (C_int) :: lammps_config_package_count
INTEGER(C_int) :: lammps_config_package_count
END FUNCTION lammps_config_package_count
FUNCTION lammps_config_package_name (idx, buffer, buf_size) BIND(C)
FUNCTION lammps_config_package_name(idx, buffer, buf_size) BIND(C)
IMPORT :: C_int, C_ptr
IMPLICIT NONE
INTEGER (C_int) :: lammps_config_package_name
INTEGER (C_int), VALUE :: idx, buf_size
TYPE (C_ptr), VALUE :: buffer
INTEGER(C_int) :: lammps_config_package_name
INTEGER(C_int), VALUE :: idx, buf_size
TYPE(C_ptr), VALUE :: buffer
END FUNCTION lammps_config_package_name
!LOGICAL FUNCTION lammps_config_accelerator
@ -503,18 +503,18 @@ MODULE LIBLAMMPS
!SUBROUTINE lammps_get_gpu_device
!LOGICAL FUNCTION lammps_has_id
!INTEGER (C_int) FUNCTION lammps_id_count
!INTEGER(C_int) FUNCTION lammps_id_count
!SUBROUTINE lammps_id_name
!INTEGER (C_int) FUNCTION lammps_plugin_count
!INTEGER(C_int) FUNCTION lammps_plugin_count
!SUBROUTINE lammps_plugin_name
!Both of these use LAMMPS_BIGBIG
!INTEGER (LAMMPS_imageint) FUNCTION lammps_encode_image_flags
!INTEGER(LAMMPS_imageint) FUNCTION lammps_encode_image_flags
!SUBROUTINE lammps_decode_image_flags
!SUBROUTINE lammps_set_fix_external_callback ! may have trouble....
!FUNCTION lammps_fix_external_get_force() ! returns real(c_double) (:)
!FUNCTION lammps_fix_external_get_force() ! returns real(c_double)(:)
!SUBROUTINE lammps_fix_external_set_energy_global
!SUBROUTINE lammps_fix_external_set_energy_peratom
@ -523,7 +523,7 @@ MODULE LIBLAMMPS
!SUBROUTINE lammps_fix_external_set_vector_length
!SUBROUTINE lammps_fix_external_set_vector
SUBROUTINE lammps_flush_buffers (handle) BIND(C)
SUBROUTINE lammps_flush_buffers(handle) BIND(C)
IMPORT :: C_ptr
IMPLICIT NONE
TYPE(C_ptr), VALUE :: handle
@ -548,19 +548,19 @@ MODULE LIBLAMMPS
TYPE(c_ptr), VALUE :: handle
END FUNCTION lammps_is_running
SUBROUTINE lammps_force_timeout (handle) BIND(C)
SUBROUTINE lammps_force_timeout(handle) BIND(C)
IMPORT :: c_ptr
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle
END SUBROUTINE lammps_force_timeout
INTEGER (C_int) FUNCTION lammps_has_error (handle) BIND(C)
INTEGER(C_int) FUNCTION lammps_has_error(handle) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle
END FUNCTION lammps_has_error
INTEGER (c_int) FUNCTION lammps_get_last_error_message &
INTEGER(c_int) FUNCTION lammps_get_last_error_message &
(handle, buffer, buf_size) BIND(C)
IMPORT :: c_ptr, c_int, c_char
IMPLICIT NONE
@ -700,14 +700,14 @@ CONTAINS
END SUBROUTINE lmp_commands_string
! equivalent function to lammps_get_natoms
REAL (c_double) FUNCTION lmp_get_natoms(self)
REAL(c_double) FUNCTION lmp_get_natoms(self)
CLASS(lammps) :: self
lmp_get_natoms = lammps_get_natoms(self%handle)
END FUNCTION lmp_get_natoms
! equivalent function to lammps_get_thermo
REAL (c_double) FUNCTION lmp_get_thermo(self,name)
REAL(c_double) FUNCTION lmp_get_thermo(self,name)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*) :: name
TYPE(C_ptr) :: Cname
@ -724,7 +724,7 @@ CONTAINS
REAL(c_double), INTENT(OUT), TARGET, OPTIONAL :: xy, yz, xz
LOGICAL, INTENT(OUT), OPTIONAL :: pflags(3), boxflag
INTEGER(c_int), TARGET :: C_pflags(3), C_boxflag
TYPE (c_ptr) :: ptr(7)
TYPE(c_ptr) :: ptr(7)
ptr = c_null_ptr
IF ( PRESENT(boxlo) ) ptr(1) = C_LOC(boxlo(1))
@ -752,7 +752,7 @@ CONTAINS
SUBROUTINE lmp_memory_usage(self,meminfo)
CLASS(lammps), INTENT(IN) :: self
INTEGER, PARAMETER :: MEMINFO_ELEM = 3
REAL (c_double), DIMENSION(MEMINFO_ELEM), INTENT(OUT) :: meminfo
REAL(c_double), DIMENSION(MEMINFO_ELEM), INTENT(OUT) :: meminfo
CALL lammps_memory_usage(self%handle,meminfo)
END SUBROUTINE lmp_memory_usage
@ -765,7 +765,7 @@ CONTAINS
END FUNCTION lmp_get_mpi_comm
! equivalent function to lammps_extract_setting
INTEGER (c_int) FUNCTION lmp_extract_setting(self, keyword)
INTEGER(c_int) FUNCTION lmp_extract_setting(self, keyword)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: keyword
TYPE(c_ptr) :: Ckeyword
@ -778,7 +778,7 @@ CONTAINS
! equivalent function to lammps_extract_global
! the assignment is actually overloaded so as to bind the pointers to
! 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), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: name
TYPE(lammps_data) :: global_data
@ -849,7 +849,7 @@ CONTAINS
! equivalent function to lammps_extract_atom
! the assignment is actually overloaded so as to bind the pointers to
! 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), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: name
TYPE(lammps_data) :: peratom_data
@ -916,7 +916,7 @@ CONTAINS
! equivalent function to lammps_extract_compute
! the assignment operator is overloaded so as to bind the pointers to
! 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), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: id
INTEGER(c_int), INTENT(IN) :: style, type
@ -980,7 +980,7 @@ CONTAINS
CALL lammps_free(Cid)
END FUNCTION lmp_extract_compute
FUNCTION lmp_extract_fix(self, id, style, type, nrow, ncol) RESULT (fix_data)
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
@ -1079,7 +1079,7 @@ CONTAINS
END FUNCTION lmp_extract_fix
! equivalent function to lammps_extract_variable
FUNCTION lmp_extract_variable(self, name, group) RESULT (variable_data)
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
@ -1157,9 +1157,9 @@ CONTAINS
END FUNCTION lmp_extract_variable
! equivalent function to lammps_set_variable
SUBROUTINE lmp_set_variable (self, name, str)
SUBROUTINE lmp_set_variable(self, name, str)
CLASS(lammps), INTENT(IN) :: self
CHARACTER (LEN=*), INTENT(IN) :: name, str
CHARACTER(LEN=*), INTENT(IN) :: name, str
INTEGER :: err
TYPE(C_ptr) :: Cstr, Cname
@ -1183,7 +1183,7 @@ CONTAINS
END FUNCTION lmp_version
! equivalent function to lammps_get_os_info
SUBROUTINE lmp_get_os_info (buffer)
SUBROUTINE lmp_get_os_info(buffer)
CHARACTER(LEN=*) :: buffer
INTEGER(c_int) :: buf_size
CHARACTER(LEN=1,KIND=c_char), DIMENSION(LEN(buffer)), TARGET :: Cbuffer
@ -1193,7 +1193,7 @@ CONTAINS
buffer = ''
ptr = C_LOC(Cbuffer(1))
buf_size = LEN(buffer)
CALL lammps_get_os_info (ptr, buf_size)
CALL lammps_get_os_info(ptr, buf_size)
DO i=1,buf_size
IF ( Cbuffer(i) == C_NULL_CHAR ) EXIT
buffer(i:i) = Cbuffer(i)
@ -1251,8 +1251,8 @@ CONTAINS
! equivalent function to lammps_config_has_package
LOGICAL FUNCTION lmp_config_has_package(name)
CHARACTER(LEN=*), INTENT(IN) :: name
INTEGER (c_int) :: has_package
TYPE (c_ptr) :: Cname
INTEGER(c_int) :: has_package
TYPE(c_ptr) :: Cname
Cname = f2c_string(name)
has_package = lammps_config_has_package(Cname)
@ -1261,7 +1261,7 @@ CONTAINS
END FUNCTION lmp_config_has_package
! equivalent subroutine to lammps_config_package_name
SUBROUTINE lmp_config_package_name (idx, buffer)
SUBROUTINE lmp_config_package_name(idx, buffer)
INTEGER, INTENT(IN) :: idx
CHARACTER(LEN=*), INTENT(OUT) :: buffer
INTEGER(c_int) :: Cidx, Csuccess
@ -1282,7 +1282,7 @@ CONTAINS
END SUBROUTINE lmp_config_package_name
! equivalent function to Python routine .installed_packages()
SUBROUTINE lmp_installed_packages (package, length)
SUBROUTINE lmp_installed_packages(package, length)
CHARACTER(LEN=:), DIMENSION(:), ALLOCATABLE, INTENT(OUT) :: package
INTEGER, INTENT(IN), OPTIONAL :: length
INTEGER, PARAMETER :: MAX_BUFFER_LENGTH = 31
@ -1317,7 +1317,7 @@ CONTAINS
END FUNCTION lmp_is_running
! equivalent function to lammps_force_timeout
SUBROUTINE lmp_force_timeout (self)
SUBROUTINE lmp_force_timeout(self)
CLASS(lammps), INTENT(IN) :: self
CALL lammps_force_timeout(self%handle)
@ -1365,7 +1365,7 @@ CONTAINS
! ----------------------------------------------------------------------
! functions to assign user-space pointers to LAMMPS data
! ----------------------------------------------------------------------
SUBROUTINE assign_int_to_lammps_data (lhs, rhs)
SUBROUTINE assign_int_to_lammps_data(lhs, rhs)
INTEGER(c_int), INTENT(OUT), POINTER :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1376,7 +1376,7 @@ CONTAINS
END IF
END SUBROUTINE assign_int_to_lammps_data
SUBROUTINE assign_int64_to_lammps_data (lhs, rhs)
SUBROUTINE assign_int64_to_lammps_data(lhs, rhs)
INTEGER(c_int64_t), INTENT(OUT), POINTER :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1387,7 +1387,7 @@ CONTAINS
END IF
END SUBROUTINE assign_int64_to_lammps_data
SUBROUTINE assign_intvec_to_lammps_data (lhs, rhs)
SUBROUTINE assign_intvec_to_lammps_data(lhs, rhs)
INTEGER(c_int), DIMENSION(:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1398,7 +1398,7 @@ CONTAINS
END IF
END SUBROUTINE assign_intvec_to_lammps_data
SUBROUTINE assign_int64vec_to_lammps_data (lhs, rhs)
SUBROUTINE assign_int64vec_to_lammps_data(lhs, rhs)
INTEGER(c_int64_t), DIMENSION(:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1409,7 +1409,7 @@ CONTAINS
END IF
END SUBROUTINE assign_int64vec_to_lammps_data
SUBROUTINE assign_double_to_lammps_data (lhs, rhs)
SUBROUTINE assign_double_to_lammps_data(lhs, rhs)
REAL(c_double), INTENT(OUT), POINTER :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1420,7 +1420,7 @@ CONTAINS
END IF
END SUBROUTINE assign_double_to_lammps_data
SUBROUTINE assign_doublevec_to_lammps_data (lhs, rhs)
SUBROUTINE assign_doublevec_to_lammps_data(lhs, rhs)
REAL(c_double), DIMENSION(:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1431,7 +1431,7 @@ CONTAINS
END IF
END SUBROUTINE assign_doublevec_to_lammps_data
SUBROUTINE assign_doublemat_to_lammps_data (lhs, rhs)
SUBROUTINE assign_doublemat_to_lammps_data(lhs, rhs)
REAL(c_double), DIMENSION(:,:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1442,7 +1442,7 @@ CONTAINS
END IF
END SUBROUTINE assign_doublemat_to_lammps_data
SUBROUTINE assign_string_to_lammps_data (lhs, rhs)
SUBROUTINE assign_string_to_lammps_data(lhs, rhs)
CHARACTER(LEN=*), INTENT(OUT) :: lhs
CLASS(lammps_data), INTENT(IN) :: rhs
@ -1456,7 +1456,7 @@ CONTAINS
! ----------------------------------------------------------------------
! functions to assign user-space pointers to LAMMPS *fix* data
! ----------------------------------------------------------------------
SUBROUTINE assign_double_to_lammps_fix_data (lhs, rhs)
SUBROUTINE assign_double_to_lammps_fix_data(lhs, rhs)
REAL(c_double), INTENT(OUT) :: lhs
CLASS(lammps_fix_data), INTENT(IN) :: rhs
@ -1467,7 +1467,7 @@ CONTAINS
END IF
END SUBROUTINE assign_double_to_lammps_fix_data
SUBROUTINE assign_doublevec_to_lammps_fix_data (lhs, rhs)
SUBROUTINE assign_doublevec_to_lammps_fix_data(lhs, rhs)
REAL(c_double), DIMENSION(:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_fix_data), INTENT(IN) :: rhs
@ -1478,7 +1478,7 @@ CONTAINS
END IF
END SUBROUTINE assign_doublevec_to_lammps_fix_data
SUBROUTINE assign_doublemat_to_lammps_fix_data (lhs, rhs)
SUBROUTINE assign_doublemat_to_lammps_fix_data(lhs, rhs)
REAL(c_double), DIMENSION(:,:), INTENT(OUT), POINTER :: lhs
CLASS(lammps_fix_data), INTENT(IN) :: rhs
@ -1492,7 +1492,7 @@ CONTAINS
! ----------------------------------------------------------------------
! functions to assign user-space pointers to LAMMPS *variable* data
! ----------------------------------------------------------------------
SUBROUTINE assign_double_to_lammps_variable_data (lhs, rhs)
SUBROUTINE assign_double_to_lammps_variable_data(lhs, rhs)
REAL(c_double), INTENT(OUT) :: lhs
CLASS(lammps_variable_data), INTENT(IN) :: rhs
@ -1503,7 +1503,7 @@ CONTAINS
END IF
END SUBROUTINE assign_double_to_lammps_variable_data
SUBROUTINE assign_doublevec_to_lammps_variable_data (lhs, rhs)
SUBROUTINE assign_doublevec_to_lammps_variable_data(lhs, rhs)
REAL(c_double), DIMENSION(:), ALLOCATABLE, INTENT(OUT) :: lhs
CLASS(lammps_variable_data), INTENT(IN) :: rhs
@ -1516,7 +1516,7 @@ CONTAINS
END IF
END SUBROUTINE assign_doublevec_to_lammps_variable_data
SUBROUTINE assign_string_to_lammps_variable_data (lhs, rhs)
SUBROUTINE assign_string_to_lammps_variable_data(lhs, rhs)
CHARACTER(LEN=*), INTENT(OUT) :: lhs
CLASS(lammps_variable_data), INTENT(IN) :: rhs
@ -1531,31 +1531,31 @@ CONTAINS
! Generic function to catch all errors in assignments of LAMMPS data to
! user-space variables/pointers
! ----------------------------------------------------------------------
SUBROUTINE assignment_error (type1, str2)
SUBROUTINE assignment_error(type1, str2)
CLASS(lammps_data_baseclass), INTENT(IN) :: type1
CHARACTER (LEN=*), INTENT(IN) :: str2
CHARACTER (LEN=:), ALLOCATABLE :: str1
CHARACTER(LEN=*), INTENT(IN) :: str2
CHARACTER(LEN=:), ALLOCATABLE :: str1
SELECT CASE (type1%datatype)
CASE (DATA_INT)
SELECT CASE(type1%datatype)
CASE(DATA_INT)
str1 = 'scalar int'
CASE (DATA_INT_1D)
CASE(DATA_INT_1D)
str1 = 'vector of ints'
CASE (DATA_INT_2D)
CASE(DATA_INT_2D)
str1 = 'matrix of ints'
CASE (DATA_INT64)
CASE(DATA_INT64)
str1 = 'scalar long int'
CASE (DATA_INT64_1D)
CASE(DATA_INT64_1D)
str1 = 'vector of long ints'
CASE (DATA_INT64_2D)
CASE(DATA_INT64_2D)
str1 = 'matrix of long ints'
CASE (DATA_DOUBLE)
CASE(DATA_DOUBLE)
str1 = 'scalar double'
CASE (DATA_DOUBLE_1D)
CASE(DATA_DOUBLE_1D)
str1 = 'vector of doubles'
CASE (DATA_DOUBLE_2D)
CASE(DATA_DOUBLE_2D)
str1 = 'matrix of doubles'
CASE (DATA_STRING)
CASE(DATA_STRING)
str1 = 'string'
CASE DEFAULT
str1 = 'that type'