Finished extract_compute and its unit tests and documentation

unittest/fortran/test_fortran_extract_compute.f90

@@ -6,10 +6,11 @@ MODULE keepcompute
       '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(2), PARAMETER :: cont_input = &
+  CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: cont_input = &
       [ CHARACTER(len=40) ::                                &
       'create_atoms 1 single &',                            &
-      ' 0.2 0.1 0.1' ]
+      ' 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',                              &
@@ -51,11 +52,13 @@ SUBROUTINE f_lammps_setup_extract_compute () BIND(C)
    CALL lmp%commands_list(pair_input)
    CALL lmp%command("compute peratompe all pe/atom") ! per-atom vector
    call lmp%command("compute stress all stress/atom thermo_temp") ! per-atom array
-   CALL lmp%command("compute COM all com") ! global vector
    CALL lmp%command("compute totalpe all reduce sum c_peratompe") ! global scalar
-   CALL lmp%command("compute 1 all rdf 100") ! global array
+   CALL lmp%command("compute COM all com") ! global vector
+   CALL lmp%command("compute RDF all rdf 100") ! global array
    CALL lmp%command("compute pairdist all pair/local dist") ! local vector
    CALL lmp%command("compute pairlocal all pair/local dist dx dy dz") ! local array
+   CALL lmp%command("thermo_style custom step pe c_totalpe c_COM[1]")
+   CALL lmp%command("run 0") ! must be here, otherwise will SEGFAULT
 END SUBROUTINE f_lammps_setup_extract_compute
 
 FUNCTION f_lammps_extract_compute_peratom_vector (i) BIND(C)
@@ -70,3 +73,80 @@ FUNCTION f_lammps_extract_compute_peratom_vector (i) BIND(C)
    vector = lmp%extract_compute('peratompe', lmp%style%atom, lmp%type%vector)
    f_lammps_extract_compute_peratom_vector = vector(i)
 END FUNCTION f_lammps_extract_compute_peratom_vector
+
+FUNCTION f_lammps_extract_compute_peratom_array (i,j) BIND(C)
+   USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
+   USE LIBLAMMPS
+   USE keepcompute, ONLY : lmp
+   IMPLICIT NONE
+   INTEGER(C_int), INTENT(IN), VALUE :: i, j
+   REAL(C_double) :: f_lammps_extract_compute_peratom_array
+   REAL(C_double), DIMENSION(:,:), POINTER :: array => NULL()
+
+   array = lmp%extract_compute('stress', lmp%style%atom, lmp%type%array)
+   f_lammps_extract_compute_peratom_array = array(i,j)
+END FUNCTION f_lammps_extract_compute_peratom_array
+
+FUNCTION f_lammps_extract_compute_global_scalar () BIND(C)
+   USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
+   USE LIBLAMMPS
+   USE keepcompute, ONLY : lmp
+   IMPLICIT NONE
+   REAL(C_double) :: f_lammps_extract_compute_global_scalar
+   REAL(C_double), POINTER :: scalar
+
+   scalar = lmp%extract_compute('totalpe', lmp%style%global, lmp%type%scalar)
+   f_lammps_extract_compute_global_scalar = scalar
+END FUNCTION f_lammps_extract_compute_global_scalar
+
+FUNCTION f_lammps_extract_compute_global_vector (i) BIND(C)
+   USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
+   USE LIBLAMMPS
+   USE keepcompute, ONLY : lmp
+   IMPLICIT NONE
+   INTEGER(c_int), INTENT(IN), VALUE :: i
+   REAL(C_double) :: f_lammps_extract_compute_global_vector
+   REAL(C_double), DIMENSION(:), POINTER :: vector
+
+   vector = lmp%extract_compute('COM', lmp%style%global, lmp%type%vector)
+   f_lammps_extract_compute_global_vector = vector(i)
+END FUNCTION f_lammps_extract_compute_global_vector
+
+FUNCTION f_lammps_extract_compute_global_array (i,j) BIND(C)
+   USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
+   USE LIBLAMMPS
+   USE keepcompute, ONLY : lmp
+   IMPLICIT NONE
+   INTEGER(c_int), INTENT(IN), VALUE :: i, j
+   REAL(C_double) :: f_lammps_extract_compute_global_array
+   REAL(C_double), DIMENSION(:,:), POINTER :: array
+
+   array = lmp%extract_compute('RDF', lmp%style%global, lmp%type%array)
+   f_lammps_extract_compute_global_array = array(i,j)
+END FUNCTION f_lammps_extract_compute_global_array
+
+FUNCTION f_lammps_extract_compute_local_vector (i) BIND(C)
+   USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
+   USE LIBLAMMPS
+   USE keepcompute, ONLY : lmp
+   IMPLICIT NONE
+   INTEGER(c_int), INTENT(IN), VALUE :: i
+   REAL(C_double) :: f_lammps_extract_compute_local_vector
+   REAL(C_double), DIMENSION(:), POINTER :: vector
+
+   vector = lmp%extract_compute('pairdist', lmp%style%local, lmp%type%vector)
+   f_lammps_extract_compute_local_vector = vector(i)
+END FUNCTION f_lammps_extract_compute_local_vector
+
+FUNCTION f_lammps_extract_compute_local_array (i, j) BIND(C)
+   USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
+   USE LIBLAMMPS
+   USE keepcompute, ONLY : lmp
+   IMPLICIT NONE
+   INTEGER(c_int), INTENT(IN), VALUE :: i, j
+   REAL(C_double) :: f_lammps_extract_compute_local_array
+   REAL(C_double), DIMENSION(:,:), POINTER :: array
+
+   array = lmp%extract_compute('pairlocal', lmp%style%local, lmp%type%array)
+   f_lammps_extract_compute_local_array = array(i,j)
+END FUNCTION f_lammps_extract_compute_local_array