From 05caf6c29434b4aa3695e557c5d40e473cae3909 Mon Sep 17 00:00:00 2001 From: Eisuke Kawashima Date: Wed, 3 Aug 2022 06:08:52 +0900 Subject: [PATCH] Fix typos and markdown syntax (#54) --- README.md | 2 +- doc/format-gen.md | 4 ++-- doc/format-qchem.md | 2 +- doc/format-tmol.md | 4 ++-- src/mctc/io/convert.f90 | 6 +++--- src/mctc/io/math.f90 | 2 +- src/mctc/io/read/pdb.f90 | 2 +- src/mctc/io/structure/info.f90 | 4 ++-- src/mctc/io/symbols.f90 | 4 ++-- src/mctc/io/write.f90 | 2 +- src/mctc/io/write/vasp.f90 | 2 +- 11 files changed, 17 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index ce45ea6c..b6f3174e 100644 --- a/README.md +++ b/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 diff --git a/doc/format-gen.md b/doc/format-gen.md index 699bb9ff..d99b8e3a 100644 --- a/doc/format-gen.md +++ b/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. diff --git a/doc/format-qchem.md b/doc/format-qchem.md index da269a18..2baa13cd 100644 --- a/doc/format-qchem.md +++ b/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. -``` diff --git a/doc/format-tmol.md b/doc/format-tmol.md index d064a4d6..0603abf4 100644 --- a/doc/format-tmol.md +++ b/doc/format-tmol.md @@ -36,7 +36,7 @@ $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. @@ -44,7 +44,7 @@ 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. diff --git a/src/mctc/io/convert.f90 b/src/mctc/io/convert.f90 index a1156169..6915f070 100644 --- a/src/mctc/io/convert.f90 +++ b/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 diff --git a/src/mctc/io/math.f90 b/src/mctc/io/math.f90 index 8073b4c6..672f35c0 100644 --- a/src/mctc/io/math.f90 +++ b/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 diff --git a/src/mctc/io/read/pdb.f90 b/src/mctc/io/read/pdb.f90 index 94881674..299e5cc4 100644 --- a/src/mctc/io/read/pdb.f90 +++ b/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) diff --git a/src/mctc/io/structure/info.f90 b/src/mctc/io/structure/info.f90 index 5f30fe69..cb3636ae 100644 --- a/src/mctc/io/structure/info.f90 +++ b/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 diff --git a/src/mctc/io/symbols.f90 b/src/mctc/io/symbols.f90 index 01c63794..069f2f34 100644 --- a/src/mctc/io/symbols.f90 +++ b/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) diff --git a/src/mctc/io/write.f90 b/src/mctc/io/write.f90 index 2ab8378e..42eeee4d 100644 --- a/src/mctc/io/write.f90 +++ b/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 diff --git a/src/mctc/io/write/vasp.f90 b/src/mctc/io/write/vasp.f90 index 6e09481d..83d7a662 100644 --- a/src/mctc/io/write/vasp.f90 +++ b/src/mctc/io/write/vasp.f90 @@ -79,7 +79,7 @@ subroutine write_vasp(self, unit, comment_line) end do write(unit, '(a)') - ! write the count of the consequtive atom types + ! write the count of the consecutive atom types do i = 1, j write(unit, '(1x, i0)', advance='no') kinds(i) end do