Add stride in the input

src/input_parser.f90

@@ -3,7 +3,7 @@ module parser_module
 
 contains
 
-    subroutine read_config(input_file, n_atoms, n_steps, dt, box_length, tolerance, max_iter)
+    subroutine read_config(input_file, n_atoms, n_steps, dt, box_length, stride)
         !
         ! Routine to read the input configuration file
         !
@@ -12,8 +12,8 @@ subroutine read_config(input_file, n_atoms, n_steps, dt, box_length, tolerance,
         integer :: num_args
         character(len=100) :: command
 
-        integer, intent(out) :: n_atoms, n_steps, max_iter
-        real(8), intent(out) :: dt, box_length, tolerance
+        integer, intent(out) :: n_atoms, n_steps, stride
+        real(8), intent(out) :: dt, box_length
 
         ! Check that CLI parameters is correct
         num_args = command_argument_count()
@@ -36,16 +36,14 @@ subroutine read_config(input_file, n_atoms, n_steps, dt, box_length, tolerance,
         read(20, *) n_steps
         read(20, *) dt
         read(20, *) box_length
-        read(20, *) tolerance
-        read(20, *) max_iter
+        read(20, *) stride
         close(20)
 
         print *, 'Number of atoms: ', n_atoms
         print *, 'Number of steps: ', n_steps
         print *, 'Time step: ', dt
         print *, 'Box length: ', box_length
-        print *, 'SHAKE Tolerance: ', tolerance
-        print *, 'SHAKE Max iterations: ', max_iter
+        print *, 'Stride: ', stride
 
         ! Remove the temporary file
         call system('rm parsed_config.tmp')

src/input_parser.py

@@ -29,14 +29,12 @@ def parse_config(file_name):
     n_steps = config.get('n_steps', '1000')
     n_atoms = config.get('n_atoms', '30')
     box_length = config.get('box_length', '10.0')
-    tolerance = config.get('tolerance', '1e-6')
-    max_iter = config.get('max_iter', '100')
+    stride = config.get('stride', '1')
 
     with open('parsed_config.tmp', 'w') as f:
         f.write(f'{n_atoms}\n')
         f.write(f'{n_steps}\n')
         f.write(f'{dt}\n')
         f.write(f'{box_length}\n')
-        f.write(f'{tolerance}\n')
-        f.write(f'{max_iter}\n')
+        f.write(f'{stride}\n')
 

src/main.f90

@@ -8,8 +8,8 @@ program md_simulation
     implicit none
 
     ! Define parameters
-    integer :: n_atoms, n_steps, step, num_args, max_iter
-    real(8) :: dt, box_length, tolerance
+    integer :: n_atoms, n_steps, step, num_args, stride
+    real(8) :: dt, box_length
     character(len=100) :: input_file, output_file, output_file_energies, command
     logical :: file_exists
 
@@ -19,7 +19,7 @@ program md_simulation
     ! Kinetic, potential and total energies
     real(8) :: ke, pe, te
 
-    call read_config(input_file, n_atoms, n_steps, dt, box_length, tolerance, max_iter)
+    call read_config(input_file, n_atoms, n_steps, dt, box_length, stride)
 
     ! Allocate the arrays
     allocate(positions(n_atoms, 3))