Minor updates

README.md

@@ -122,7 +122,7 @@ and [asciidoctor](https://asciidoctor.org/) for the command line interface manpa
 For generating the main documentation pages, install the documentation dependencies with
 
 ```
-pip install -f doc/requirements.txt
+pip install -r doc/requirements.txt
 ```
 
 The pages can be built with
@@ -137,7 +137,7 @@ To view the final pages you can start a HTTP server via
 python -m http.server -d _docs
 ```
 
-And open the shown URL in a browser.
+And open the shown URL in a browser (usually this is https://localhost:8000).
 The documentation is automatically deployed from the main branch and can be viewed on [readthedocs](https://dftd3.readthedocs.io/).
 
 
@@ -180,7 +180,7 @@ In case you want to access the DFT-D3 results from other programs, dump the resu
 (the ``--noedisp`` flag prevents the ``.EDISP`` file generation):
 
 ```
-s-dftd3 --bj pbe0 --atm --json --noedisp --grad -- struct.xyz
+s-dftd3 --bj pbe0 --atm --json --grad --noedisp struct.xyz
 ```
 
 Dispersion related properties can be calculated as well:

app/cli.f90

@@ -165,14 +165,26 @@ subroutine get_run_arguments(config, list, start, error)
    type(error_type), allocatable, intent(out) :: error
 
    integer :: iarg, narg
+   logical :: read_args
    character(len=:), allocatable :: arg
 
+   read_args = .true.
    iarg = start
    narg = len(list)
    do while(iarg < narg)
       iarg = iarg + 1
       call list%get(iarg, arg)
+      if (.not.read_args) then
+         if (.not.allocated(config%input)) then
+            call move_alloc(arg, config%input)
+            cycle
+         end if
+         call fatal_error(error, "Too many positional arguments present")
+         exit
+      end if
       select case(arg)
+      case("--")
+         read_args = .false.
       case("--help")
          call info_message(error, run_help_text)
          exit

app/meson.build

@@ -33,6 +33,7 @@ if os != 'windows'
   test('help', sdftd3_exe, args: '--help', suite: 'app')
   test('noargs', sdftd3_exe, should_fail: true, suite: 'app')
   test('example', sdftd3_exe, args: files('example.xyz'), suite: 'app')
+  test('run-example', sdftd3_exe, args: ['run', '--', files('example.xyz')], suite: 'app')
   test('param-all', sdftd3_exe, args: ['param', sdftd3_parameters], suite: 'app')
   test('param-select', sdftd3_exe, args: ['param', sdftd3_parameters, 'b2plyp'], suite: 'app')
 endif

docs.md

@@ -65,7 +65,7 @@ subroutine calc_dftd3(mol, method, energy, gradient, sigma, error)
 
    call get_rational_damping(inp, method, error, s9=1.0_wp)
    if (allocated(error)) return
-   call new_rational_damping(param, inp, mol)
+   call new_rational_damping(param, inp)
 
    call new_d3_model(disp, mol)
 

test/validation/02-energy-d3-zero.resp

@@ -1,3 +1,4 @@
+run
 $ORIGIN/02-ser-xad.gen
 --zero
 b3lyp