Merge pull request #15 from comecattin/parser

Better parser

.gitignore

@@ -39,6 +39,7 @@ bin/
 *.arc
 trajectories.dat
 input.dat
+input.in
 energies.dat
 energies.pdf
 md_simulation

README.md

@@ -1,4 +1,5 @@
 # F-MD, Fortran Molecular Dynamic
+
 <p align='center'>
   <img src=https://github.com/comecattin/F-MD/assets/75748278/1d46d2ed-7f07-4c99-9086-a80ddbaf25b5>
 </p>
@@ -25,16 +26,18 @@ make
 
 ## Run an MD simulation
 
-To run an MD simulation simply run `./md_simulation input.dat` in the `src` directory.
+To run an MD simulation simply run `./md_simulation input.in` in the `src` directory.
 
-The file `input.dat` is the input file and contain in the following order:
+The file `input.in` is the input file and contain:
 
-- The number of particles
-- The number of time steps
-- The time step
-- The box length
+- The number of particles (`n_atoms`, default `30`)
+- The number of time steps (`n_steps`, default `1000`)
+- The time step (`dt`, default `0.001`)
+- The box length (`box_length`, default `10.0`)
+- The tolerance of the SHAKE algorithm for angle and bonds length constraints (`tolerance`, default `1e-6`)
+- The maximum number of iteration for the SHAKE algorithm (`max_iter`, default `100`)
 
-An example is given in the `examples/example_input.dat` file.
+An example is given in the `examples/example_input.in` file.
 
 ## Output and plot the trajectories
 

examples/example_input.in

@@ -0,0 +1,6 @@
+n_atoms : 30          # Number of atoms in the system
+n_steps : 10000       # Number of time steps
+dt : 0.001            # Time step
+box_length : 10.0     # Length of the PBC box
+tolerance : 1.0e-6    # SHAKE tolerance
+max_iter : 100        # Maximum iteration for SHAKE algorithm

src/input_parser.f90

@@ -0,0 +1,55 @@
+module parser_module
+    implicit none
+
+contains
+
+    subroutine read_config(input_file, n_atoms, n_steps, dt, box_length, tolerance, max_iter)
+        !
+        ! Routine to read the input configuration file
+        !
+        character(len=100):: input_file
+
+        integer :: num_args
+        character(len=100) :: command
+
+        integer, intent(out) :: n_atoms, n_steps, max_iter
+        real(8), intent(out) :: dt, box_length, tolerance
+
+        ! Check that CLI parameters is correct
+        num_args = command_argument_count()
+        if (num_args /= 1) then
+            print *, 'Usage: ./md_simulation input_file'
+            stop
+        else
+            call get_command_argument(1, input_file)
+            print *, 'Input file: ', input_file
+        end if
+
+        ! Create the python command
+        write(command, '(A, A)') 'python input_parser.py ', trim(input_file)
+        call system(command)
+
+        ! Read the temporary file created by python 
+        input_file = 'parsed_config.tmp'
+        open(unit=20, file=input_file)
+        read(20, *) n_atoms
+        read(20, *) n_steps
+        read(20, *) dt
+        read(20, *) box_length
+        read(20, *) tolerance
+        read(20, *) max_iter
+        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
+
+        ! Remove the temporary file
+        call system('rm parsed_config.tmp')
+
+
+    end subroutine read_config
+end module parser_module

src/input_parser.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+"""Parsing of the input file."""
+import argparse
+
+def parse_config(file_name):
+
+    config = {}
+
+    with open(file_name, 'r') as f:
+        for line in f:
+            line = line.strip()
+            if not line or line.startswith('#'):
+                continue
+            key, value = line.split(':', 1)
+            value = value.split('#', 1)[0].strip()
+            config[key.strip()] = value.strip()
+
+    return config
+
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Parsing of the input file")
+    parser.add_argument("file_name", help="Path to the input file")
+    args = parser.parse_args()
+    config = parse_config(args.file_name)
+
+    dt = config.get('dt', '0.001')
+    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')
+
+    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')
+

src/main.f90

@@ -1,4 +1,5 @@
 program md_simulation
+    use parser_module, only : read_config
     use initialization_module, only : initialize, initialize_water
     use forces_module, only : compute_forces, compute_forces_water
     use energies_module
@@ -9,7 +10,7 @@ program md_simulation
     ! Define parameters
     integer :: n_atoms, n_steps, step, num_args, max_iter
     real(8) :: dt, box_length, tolerance
-    character(len=100) :: input_file, output_file, output_file_energies
+    character(len=100) :: input_file, output_file, output_file_energies, command
     logical :: file_exists
 
     ! Define position, velocity and forces arrays
@@ -18,32 +19,7 @@ program md_simulation
     ! Kinetic, potential and total energies
     real(8) :: ke, pe, te
 
-    num_args = command_argument_count()
-    if (num_args /= 1) then
-        print *, 'Usage: ./md_simulation input_file'
-        stop
-    else
-        call get_command_argument(1, input_file)
-        print *, 'Input file: ', input_file
-    end if
-
-    ! Read the input parameters
-    open(unit=20, file=input_file)
-    read(20, *) n_atoms
-    read(20, *) n_steps
-    read(20, *) dt
-    read(20, *) box_length
-    read(20, *) tolerance
-    read(20, *) max_iter
-    close(20)
-
-    ! Print the input parameters
-    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
+    call read_config(input_file, n_atoms, n_steps, dt, box_length, tolerance, max_iter)
 
     ! Allocate the arrays
     allocate(positions(3, n_atoms))

src/makefile

@@ -1,5 +1,5 @@
 FC = gfortran
-OBJ = initialization.o forces.o contraints.o integration.o output_module.o  energies.o main.o
+OBJ = input_parser.o initialization.o forces.o contraints.o integration.o output_module.o  energies.o main.o
 
 md_simulation: $(OBJ)
 	$(FC) -o md_simulation $(OBJ)
@@ -25,6 +25,9 @@ output_module.o: output_module.f90
 contraints.o: contraints.f90
 	$(FC) -c contraints.f90
 
+input_parser.o: input_parser.f90
+	$(FC) -c input_parser.f90
+
 clean:
 	rm -f *.o *.mod md_simulation trajectories.dat