Implement C-API and internal parameter storage

Author: awvwgk

.github/dco.yml

@@ -0,0 +1,2 @@
+require:
+  members: false

.github/workflows/build.yml

@@ -0,0 +1,51 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        gcc_v: [9] # Version of GCC we want to use.
+
+    env:
+      FC: gfortran
+      GCC_V: ${{ matrix.gcc_v }}
+      OMP_NUM_THREADS: 2,1
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+
+    - name: Install GCC (OSX)
+      if: contains(matrix.os, 'macos')
+      run: |
+          ln -s /usr/local/bin/gfortran-${GCC_V} /usr/local/bin/gfortran
+          which gfortran-${GCC_V}
+          which gfortran
+
+    - name: Install GCC (Linux)
+      if: contains(matrix.os, 'ubuntu')
+      run: |
+        sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \
+        --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} \
+        --slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V}
+
+    - name: Install meson
+      run: pip3 install meson ninja
+
+    - name: Configure build
+      run: meson setup _build -Dopenmp=false
+
+    - name: Build library
+      run: meson compile -C _build
+
+    - name: Run unit tests
+      run: meson test -C _build --print-errorlogs --no-rebuild

README.md

@@ -10,6 +10,7 @@ and [*JCC* **32**, 1456 (2011)](https://dx.doi.org/10.1002/jcc.21759) for detail
 It is mostly based on the [`dftd4`](https://github.com/dftd4/dftd4) program and
 borrows one or two ideas from the implementation in [`ased3`](https://github.com/ehermes/ased3).
 
+
 ## Installation
 
 To build this project from the source code in this repository you need to have
@@ -46,6 +47,31 @@ This might require administrator access.
 You can alter the install prefix by ``meson configure _build --prefix=/path/to/install``.
 
 
+## Usage
+
+DFT-D3 calculations can be performed with the ``s-dftd3`` binary.
+To calculate the dispersion correction for PBE0-D3(BJ)-ATM run:
+
+```
+s-dftd3 --bj pbe0 --atm coord
+```
+
+In case you want to access the DFT-D3 results from other programs, dump the results to JSON with
+(the ``--noedisp`` flag prevents the ``.EDISP`` file generation):
+
+```
+s-dftd3 --bj pbe0 --atm --json --noedisp --grad struct.xyz
+```
+
+Dispersion related properties can be calculated as well:
+
+```
+s-dftd3 --property geo.gen
+```
+
+For an overview over all command line arguments use the ``--help`` argument.
+
+
 ## License
 
 This project is free software: you can redistribute it and/or modify it under

app/example.xyz

@@ -0,0 +1,26 @@
+  24
+        -42.15450736
+ C         -3.2624567556       -1.0740397867       -0.0000043734
+ N         -2.2754344008       -0.0292896574        0.0000359020
+ C         -0.9120851382       -0.2075386125       -0.0004880509
+ C         -0.3749333299        1.0720554184       -0.0001564184
+ N         -1.3570794708        1.9998111614        0.0003858762
+ C         -2.4726070186        1.3013159995        0.0005402177
+ H         -3.4474896946        1.7467507266        0.0010080843
+ N          0.9669701935        1.2880523079       -0.0003374012
+ C          1.8275740716        0.2107859932       -0.0000027214
+ O          3.0306801280        0.3524772071        0.0002192165
+ N          1.2570001166       -1.0570195560       -0.0000714961
+ C         -0.0994181855       -1.3854842224       -0.0003307823
+ O         -0.4879332634       -2.5400052828       -0.0002686844
+ C          2.2118766147       -2.1535108670        0.0005997875
+ H          1.6458936552       -3.0819689593        0.0002644601
+ H          2.8452151680       -2.0921377814       -0.8838098923
+ H          2.8439724684       -2.0920881626        0.8858951171
+ C          1.4878336345        2.6373781425       -0.0003075130
+ H          1.1373305002        3.1659703185       -0.8863920642
+ H          1.1383298601        3.1656042978        0.8863960393
+ H          2.5739975007        2.5744621695       -0.0008973695
+ H         -3.8918239831       -1.0020514766       -0.8884978421
+ H         -3.8928014413       -1.0010907638        0.8876971655
+ H         -2.7437217829       -2.0316581902        0.0007283419

app/main.f90

@@ -1,5 +1,5 @@
 ! This file is part of s-dftd3.
-! SPDX-Identifier: LGLP-3.0-or-later
+! SPDX-Identifier: LGPL-3.0-or-later
 !
 ! s-dftd3 is free software: you can redistribute it and/or modify it under
 ! the terms of the GNU Lesser General Public License as published by
@@ -20,12 +20,14 @@ program dftd3_main
    use mctc_io
    use dftd3
    use dftd3_output
+   use dftd3_utils
    implicit none
    character(len=*), parameter :: prog_name = "s-dftd3"
 
    type :: d3_config
-      logical :: json = .true.
+      logical :: json = .false.
       character(len=:), allocatable :: json_output
+      logical :: wrap = .true.
       logical :: tmer = .true.
       logical :: properties = .false.
       logical :: atm = .false.
@@ -49,37 +51,64 @@ program dftd3_main
    character(len=:), allocatable :: method
    type(zero_damping_param), allocatable :: zparam
    type(rational_damping_param), allocatable :: rparam
+   real(wp), allocatable :: s9
    integer :: stat, unit
    logical :: echo, exist
 
    call get_arguments(input, input_format, config, method, inp, echo, error)
    if (allocated(error)) then
-      write(error_unit, '(a)') error%message
+      write(error_unit, '("[Error]", 1x, a)') error%message
       error stop
    end if
 
+   if (config%verbosity > 1) then
+      call header(output_unit)
+   end if
+
    if (input == "-") then
       if (.not.allocated(input_format)) input_format = filetype%xyz
       call read_structure(mol, input_unit, input_format, error)
    else
       call read_structure(mol, input, error, input_format)
    end if
    if (allocated(error)) then
-      write(error_unit, '(a)') error%message
+      write(error_unit, '("[Error]", 1x, a)') error%message
       error stop
    end if
+   if (config%wrap) then
+      call wrap_to_central_cell(mol%xyz, mol%lattice, mol%periodic)
+   end if
 
+   if (config%atm) s9 = inp%s9
    if (config%zero) then
+      if (.not.config%has_param) then
+         call get_zero_damping_param(inp, method, error, s9)
+         if (allocated(error)) then
+            write(error_unit, '("[Error]", 1x, a)') error%message
+            error stop
+         end if
+      end if
       allocate(zparam)
       call new_zero_damping(zparam, inp, mol%num)
       call move_alloc(zparam, param)
    end if
    if (config%rational) then
+      if (.not.config%has_param) then
+         call get_rational_damping_param(inp, method, error, s9)
+         if (allocated(error)) then
+            write(error_unit, '("[Error]", 1x, a)') error%message
+            error stop
+         end if
+      end if
       allocate(rparam)
       call new_rational_damping(rparam, inp, mol%num)
       call move_alloc(rparam, param)
    end if
 
+   if (allocated(param) .and. config%verbosity > 0) then
+      call ascii_damping_param(output_unit, param, method)
+   end if
+
    if (config%grad) then
       allocate(gradient(3, mol%nat))
    end if
@@ -186,6 +215,19 @@ subroutine property_calc(unit, mol, disp, verbosity)
 end subroutine property_calc
 
 
+subroutine header(unit)
+   integer, intent(in) :: unit
+   character(len=:), allocatable :: version_string
+
+   call get_dftd3_version(string=version_string)
+   write(unit, '(a)') &
+      "-----------------------------------", &
+      " s i m p l e   D F T - D 3  v"// version_string, &
+      "-----------------------------------", ""
+
+end subroutine header
+
+
 subroutine help(unit)
    integer, intent(in) :: unit
 
@@ -195,21 +237,20 @@ subroutine help(unit)
    write(unit, '(a)') &
       "", &
       "Takes an geometry input to calculate the D3 dispersion correction.", &
-      "Periodic calculations are performed automatically for periodic input formats", &
+      "Periodic calculations are performed automatically for periodic input formats.", &
       "Specify the functional to select the correct parameters.", &
       ""
 
    write(unit, '(2x, a, t25, a)') &
       "-i, --input <format>", "Hint for the format of the input file", &
-      "--func <method>", "Specify functional to use", &
-      "--bj", "Use rational (Becke-Johnson) damping function", &
+      "--bj <method>", "Use rational (Becke-Johnson) damping function", &
       "--bj-param <list>", "Specify parameters for rational damping,", &
       "", "expected order is s6, s8, a1, a2 (requires four arguments)", &
-      "--zero", "Use zero (Chai-Head-Gordon) damping function", &
-      "--zero-param <list>", "Specify functional to use,", &
+      "--zero <method>", "Use zero (Chai-Head-Gordon) damping function", &
+      "--zero-param <list>", "Specify parameters for zero damping,", &
       "", "expected order is s6, s8, rs6 (requires three arguments)", &
-      "--atm", "Use ATM three-body dispersion,", &
-      "--atm-scale <s9>", "Use scaled ATM three-body dispersion,", &
+      "--atm", "Use ATM three-body dispersion", &
+      "--atm-scale <s9>", "Use scaled ATM three-body dispersion", &
       "--noedisp", "Disable writing of dispersion energy to .EDISP file", &
       "--json [file]", "Dump results to JSON output (default: dftd3.json)", &
       "--grad", "Request gradient evaluation", &
@@ -340,7 +381,11 @@ subroutine get_arguments(input, input_format, config, method, inp, echo, error)
             call move_alloc(arg, input)
             cycle
          end if
-         call fatal_error(error, "Too many positional arguments present")
+         if (arg(1:1) == "-") then
+            call fatal_error(error, "Unknown argument encountered: '"//arg//"'")
+         else
+            call fatal_error(error, "Too many positional arguments present")
+         end if
          exit
       case("-i", "--input")
          iarg = iarg + 1
@@ -352,6 +397,7 @@ subroutine get_arguments(input, input_format, config, method, inp, echo, error)
          input_format = get_filetype("."//arg)
       case("--json")
          config%json = .true.
+         config%json_output = "dftd3.json"
          iarg = iarg + 1
          call get_argument(iarg, arg)
          if (allocated(arg)) then
@@ -360,13 +406,13 @@ subroutine get_arguments(input, input_format, config, method, inp, echo, error)
                cycle
             end if
             call move_alloc(arg, config%json_output)
-         else
-            config%json_output = "dftd3.json"
          end if
       case("--property")
          config%properties = .true.
       case("--noedisp")
          config%tmer = .false.
+      case("--nowrap")
+         config%wrap = .false.
       case("--grad")
          config%grad = .true.
       case("--atm")
@@ -377,6 +423,15 @@ subroutine get_arguments(input, input_format, config, method, inp, echo, error)
          call get_argument_as_real(iarg, inp%s9, error)
          if (allocated(error)) exit
          config%atm = .true.
+      case("--zero")
+         config%zero = .true.
+         iarg = iarg + 1
+         call get_argument(iarg, arg)
+         if (.not.allocated(arg)) then
+            call fatal_error(error, "Missing argument for method")
+            exit
+         end if
+         call move_alloc(arg, method)
       case("--zero-param")
          config%zero = .true.
          config%has_param = .true.
@@ -389,6 +444,15 @@ subroutine get_arguments(input, input_format, config, method, inp, echo, error)
          iarg = iarg + 1
          call get_argument_as_real(iarg, inp%rs6, error)
          if (allocated(error)) exit
+      case("--bj")
+         config%rational = .true.
+         iarg = iarg + 1
+         call get_argument(iarg, arg)
+         if (.not.allocated(arg)) then
+            call fatal_error(error, "Missing argument for method")
+            exit
+         end if
+         call move_alloc(arg, method)
       case("--bj-param")
          config%rational = .true.
          config%has_param = .true.
@@ -404,16 +468,9 @@ subroutine get_arguments(input, input_format, config, method, inp, echo, error)
          iarg = iarg + 1
          call get_argument_as_real(iarg, inp%a2, error)
          if (allocated(error)) exit
-      case("--func")
-         iarg = iarg + 1
-         call get_argument(iarg, arg)
-         if (.not.allocated(arg)) then
-            call fatal_error(error, "Missing argument for method")
-            exit
-         end if
-         call move_alloc(arg, method)
       end select
    end do
+   if (allocated(error)) return
 
    if (.not.config%has_param .and. .not.allocated(method)) then
       config%properties = .true.

app/meson.build

@@ -20,3 +20,12 @@ sdftd3_exe = executable(
   dependencies: sdftd3_dep,
   install: install,
 )
+
+if os != 'windows'
+  test('app-version', sdftd3_exe, args: '--version')
+  test('app-help', sdftd3_exe, args: '--help')
+  test('app-noargs', sdftd3_exe, should_fail: true)
+  test('app-example', sdftd3_exe, args: files('example.xyz'))
+  test('app-zero', sdftd3_exe, args: ['--json', '--zero-param', '1.0', '1.868', '1.613', files('example.xyz')])
+  test('app-rational', sdftd3_exe, args: ['--bj-param', '1.0', '1.2576', '0.3768', '4.5865', files('example.xyz')])
+endif

config/meson.build

@@ -25,6 +25,9 @@ endif
 
 fc = meson.get_compiler('fortran')
 fc_id = fc.get_id()
+if has_cc and not get_option('python')
+  has_cc = fc_id == meson.get_compiler('c').get_id()
+endif
 
 if fc_id == 'gcc'
   add_project_arguments(
@@ -46,6 +49,11 @@ elif fc_id == 'pgi'
   )
 endif
 
+if get_option('openmp')
+  omp_dep = dependency('OpenMP')
+  lib_deps += omp_dep
+endif
+
 # Create the tool chain library as subproject
 mctc_prj = subproject(
   'mctc-lib',