Fix typos and markdown syntax (#54)

Author: e-kwsm

README.md

@@ -214,7 +214,7 @@ Error: Cannot read charges
    |
 ```
 
-4. Turbomole input with confliciting data groups
+4. Turbomole input with conflicting data groups
 
 ```
 Error: Conflicting lattice and cell groups

doc/format-gen.md

@@ -20,12 +20,12 @@ of the atomic coordinates by this index rather than their element symbol.
 
 The following lines are specified as two integers and three reals separated by
 spaces. The first integer is currently ignored. The second integer references
-the the element symbol in the second line.
+the element symbol in the second line.
 The atomic coordinates are given in Ångström for cluster, supercell and helical,
 while they are given as fraction of the lattice vector for fractional input types.
 
 For supercell and fractional input the next lines contains three reals containing
-the origin of the stucture, followed by three lines of each three reals for the
+the origin of the structure, followed by three lines of each three reals for the
 lattice vectors.
 
 Lines starting with the ``#`` are comments and are ignored while parsing.

doc/format-qchem.md

@@ -42,6 +42,7 @@ $molecule
  H         4.40230000000000       -5.15920000000000        0.82840000000000
  H         4.40020000000000       -5.16930000000000       -0.94780000000000
 $end
+```
 
 
 ## Missing Features
@@ -53,4 +54,3 @@ Following features are missing
 
 @Note Feel free to contribute support for missing features
       or bring missing features to our attention by opening an issue.
-```

doc/format-tmol.md

@@ -36,15 +36,15 @@ $end
 The ``coord`` data group contains the cartesian coordinates of all atoms and
 their element symbols at the end of each line.
 Atomic coordinates can either be specified in Bohr, by default or with the ``bohr``
-modifier on the ``coord`` data group, in Ångström with the modifer ``angs`` or
+modifier on the ``coord`` data group, in Ångström with the modifier ``angs`` or
 as fractions of the lattice vectors with the modifier ``frac``.
 Fractional coordinates can only be present for periodicities greater than zero.
 
 The periodicity of the system is specified as modifier to the ``periodic`` data
 group, the group itself is empty.
 
 The lattice parameters can either be specified in the ``lattice`` or the ``cell``
-data group, which requre different amounts of entries depending on the systems
+data group, which require different amounts of entries depending on the systems
 periodicity. Both data groups are either given in atomic units (Bohr) or in
 Ångström with the ``angs`` modifier.
 

src/mctc/io/convert.f90

@@ -19,7 +19,7 @@ module mctc_io_convert
    implicit none
    private
 
-   !> Reducted Planck's constant
+   !> Reduced Planck's constant
    real(wp), parameter :: hbar = codata%h/(2.0_wp*pi) ! J·s = kg·m²·s⁻¹
 
    !> Bohr radius
@@ -40,10 +40,10 @@ module mctc_io_convert
    !> Conversion factor from electron volts to hartree
    real(wp), public, parameter :: evtoau = 1.0_wp/autoev
 
-   !> Coversion factor between calorine and joule
+   !> Conversion factor between calorie and joule
    real(wp), public, parameter :: caltoj = 4.184_wp
 
-   !> Coversion factor between joule and calorine
+   !> Conversion factor between joule and calorie
    real(wp), public, parameter :: jtocal = 1.0_wp/caltoj
 
    !> Conversion from hartree to kJ/mol

src/mctc/io/math.f90

@@ -58,7 +58,7 @@ pure function matinv_3x3(a) result(b)
 end function matinv_3x3
 
 
-!> Determinat of 3×3 matrix
+!> Determinant of 3×3 matrix
 pure function matdet_3x3(a) result (det)
 
    !> Matrix

src/mctc/io/read/pdb.f90

@@ -42,7 +42,7 @@ subroutine read_pdb(self, unit, error)
    !> Error handling
    type(error_type), allocatable, intent(out) :: error
 
-   integer, parameter :: p_initial_size = 1000 ! this is going to be a proteine
+   integer, parameter :: p_initial_size = 1000 ! this is going to be a protein
 
    integer :: iatom, jatom, iresidue, try, stat, atom_type, pos, lnum
    real(wp) :: occ, temp, coords(3)

src/mctc/io/structure/info.f90

@@ -73,10 +73,10 @@ module mctc_io_structure_info
       !> SDF hydrogen query present or PDB without hydrogen atoms found
       logical :: missing_hydrogen = .false.
 
-      !> Periodic coordinates should use preferrably cartesian coordinates
+      !> Periodic coordinates should use preferably cartesian coordinates
       logical :: cartesian = .true.
 
-      !> Lattice information should use preferrably lattice vectors
+      !> Lattice information should use preferably lattice vectors
       logical :: lattice = .true.
 
       !> Unit of the lattice vectors should be in Angstrom if possible

src/mctc/io/symbols.f90

@@ -339,7 +339,7 @@ pure function find_number(list, number) result(position)
 end function find_number
 
 
-!> Append an element symbol to an unsorted list, to ensure no dublicates search
+!> Append an element symbol to an unsorted list, to ensure no duplicates search
 !> for the element symbol first
 pure subroutine append_symbol(list, nlist, symbol)
 
@@ -362,7 +362,7 @@ pure subroutine append_symbol(list, nlist, symbol)
 end subroutine append_symbol
 
 
-!> Append an atomic number to an unsorted list, to ensure no dublicates search
+!> Append an atomic number to an unsorted list, to ensure no duplicates search
 !> for the atomic number first
 pure subroutine append_number(list, nlist, number)
 

src/mctc/io/write.f90

@@ -70,7 +70,7 @@ subroutine write_structure_to_file(self, file, error, format)
       ftype = get_filetype(file)
    end if
 
-   ! Unknown file type is inacceptable in this situation,
+   ! Unknown file type is unacceptable in this situation,
    ! try to figure at least something out
    if (ftype == filetype%unknown) then
       if (any(self%periodic)) then