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Add pymatgen writer
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‎man/mctc-convert.1.adoc‎

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@@ -28,6 +28,7 @@ Supported formats:
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- Gaussian's external program input (ein)
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- JSON input with `qcschema_molecule` or `qcschema_input` structure (json)
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- Chemical JSON input (cjson)
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- Pymatgen JSON with `Molecule` or `Structure` schema (pmgjson)
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- FHI-AIMS' input files (geometry.in)
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- Q-Chem molecule block inputs (qchem)
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‎src/mctc/io/read.f90‎

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@@ -23,6 +23,7 @@ module mctc_io_read
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use mctc_io_read_qchem, only : read_qchem
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use mctc_io_read_qcschema, only : read_qcschema
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use mctc_io_read_pdb, only : read_pdb
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use mctc_io_read_pymatgen, only : read_pymatgen
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use mctc_io_read_turbomole, only : read_coord
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use mctc_io_read_vasp, only : read_vasp
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use mctc_io_read_xyz, only : read_xyz
@@ -156,6 +157,9 @@ subroutine get_structure_reader(reader, ftype)
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case(filetype%pdb)
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reader => read_pdb
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case(filetype%pymatgen)
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reader => read_pymatgen
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case(filetype%gen)
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reader => read_genformat
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‎src/mctc/io/write.f90‎

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@@ -21,6 +21,7 @@ module mctc_io_write
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use mctc_io_write_gaussian, only : write_gaussian_external
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use mctc_io_write_genformat, only : write_genformat
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use mctc_io_write_pdb, only : write_pdb
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use mctc_io_write_pymatgen, only : write_pymatgen
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use mctc_io_write_qchem, only : write_qchem
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use mctc_io_write_qcschema, only : write_qcschema
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use mctc_io_write_turbomole, only : write_coord
@@ -117,6 +118,9 @@ subroutine write_structure_to_unit(self, unit, ftype, error)
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case(filetype%pdb)
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call write_pdb(self, unit)
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case(filetype%pymatgen)
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call write_pymatgen(self, unit)
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case(filetype%gen)
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call write_genformat(self, unit)
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‎src/mctc/io/write/CMakeLists.txt‎

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@@ -22,6 +22,7 @@ list(
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"${dir}/gaussian.f90"
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"${dir}/genformat.f90"
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"${dir}/pdb.f90"
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"${dir}/pymatgen.f90"
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"${dir}/qchem.f90"
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"${dir}/qcschema.f90"
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"${dir}/turbomole.f90"

‎src/mctc/io/write/meson.build‎

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@@ -19,6 +19,7 @@ srcs += files(
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'gaussian.f90',
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'genformat.f90',
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'pdb.f90',
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'pymatgen.f90',
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'qchem.f90',
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'qcschema.f90',
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'turbomole.f90',

‎src/mctc/io/write/pymatgen.f90‎

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@@ -0,0 +1,332 @@
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! This file is part of mctc-lib.
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!
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! Licensed under the Apache License, Version 2.0 (the "License");
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! you may not use this file except in compliance with the License.
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! You may obtain a copy of the License at
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!
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! http://www.apache.org/licenses/LICENSE-2.0
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!
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! Unless required by applicable law or agreed to in writing, software
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! distributed under the License is distributed on an "AS IS" BASIS,
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! WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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! See the License for the specific language governing permissions and
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! limitations under the License.
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module mctc_io_write_pymatgen
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use mctc_env_accuracy, only : wp
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use mctc_io_convert, only : autoaa
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use mctc_io_math, only : matinv_3x3, matdet_3x3
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use mctc_io_structure, only : structure_type
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use mctc_version, only : get_mctc_version
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implicit none
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private
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public :: write_pymatgen
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interface json_value
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module procedure :: json_value_char
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module procedure :: json_value_int
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module procedure :: json_value_real
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end interface json_value
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interface json_array
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module procedure :: json_array_char_1
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module procedure :: json_array_int_1
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module procedure :: json_array_real_1
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end interface json_array
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character(len=*), parameter :: nl = new_line('a')
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contains
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subroutine write_pymatgen(mol, unit)
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type(structure_type), intent(in) :: mol
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integer, intent(in) :: unit
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write(unit, '(a)') json_string(mol, " ")
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end subroutine write_pymatgen
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pure function json_string(mol, indent) result(string)
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type(structure_type), intent(in) :: mol
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character(len=*), intent(in), optional :: indent
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character(len=:), allocatable :: string
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integer :: iat, isp, ilt
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real(wp) :: cellpar(6), volume, vec(3)
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real(wp), allocatable :: invlat(:, :)
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string = "{"
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if (present(indent)) string = string // nl // indent
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string = string // json_key("@module", indent) // json_value("pymatgen.core.structure")
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string = string // ","
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if (present(indent)) string = string // nl // indent
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if (any(mol%periodic)) then
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string = string // json_key("@class", indent) // json_value("Structure")
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invlat = matinv_3x3(mol%lattice)
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else
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string = string // json_key("@class", indent) // json_value("Molecule")
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string = string // ","
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if (present(indent)) string = string // nl // indent
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string = string // json_key("charge", indent) // json_value(nint(mol%charge))
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string = string // ","
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if (present(indent)) string = string // nl // indent
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string = string // json_key("spin_multiplicity", indent) // json_value(mol%uhf + 1)
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end if
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string = string // ","
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if (present(indent)) string = string // nl // indent
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string = string // json_key("sites", indent) // "["
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do iat = 1, mol%nat
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isp = mol%id(iat)
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if (present(indent)) string = string // nl // indent // indent
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string = string // "{"
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if (present(indent)) string = string // nl // indent // indent // indent
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string = string // json_key("name", indent) // json_value(trim(mol%sym(isp)))
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string = string // ","
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if (present(indent)) string = string // " "
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string = string // json_key("label", indent) // json_value(trim(mol%sym(isp)))
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string = string // ","
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if (present(indent)) string = string // " "
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string = string // json_key("species", indent) // "[{"
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string = string // json_key("element", indent) // json_value(trim(mol%sym(isp))) // ","
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if (present(indent)) string = string // " "
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string = string // json_key("occu", indent) // json_value(1)
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string = string // "}]"
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string = string // ","
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if (present(indent)) string = string // nl // indent // indent // indent
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string = string // json_key("xyz", indent) // &
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& "[" // json_value(mol%xyz(1, iat) * autoaa, '(es23.16)') // "," // &
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& json_value(mol%xyz(2, iat) * autoaa, '(es23.16)') // "," // &
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& json_value(mol%xyz(3, iat) * autoaa, '(es23.16)') // "]"
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! if (allocated(invlat)) then
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! vec = matmul(invlat, mol%xyz(:, iat))
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! if (present(indent)) string = string // nl // indent // indent // indent
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! string = string // json_key("abc", indent) // &
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! & "[" // json_value(vec(1), '(es23.16)') // "," // &
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! & json_value(vec(2), '(es23.16)') // "," // &
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! & json_value(vec(3), '(es23.16)') // "]"
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! end if
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string = string // ","
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if (present(indent)) string = string // nl // indent // indent // indent
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string = string // json_key("properties", indent) // "{}"
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if (present(indent)) string = string // nl // indent // indent
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string = string // "}"
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if (iat /= mol%nat) then
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string = string // ","
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end if
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end do
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if (present(indent)) string = string // nl // indent
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string = string // "]"
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if (any(mol%periodic)) then
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call dlat_to_cell(mol%lattice, cellpar)
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volume = matdet_3x3(mol%lattice)
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string = string // ","
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if (present(indent)) string = string // nl // indent
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string = string // json_key("lattice", indent) // "{"
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("matrix", indent) // "["
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if (present(indent)) string = string // nl // indent // indent // indent
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do ilt = 1, 3
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string = string // "[" // &
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& json_value(mol%lattice(1, ilt) * autoaa, '(es23.16)') // "," // &
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& json_value(mol%lattice(2, ilt) * autoaa, '(es23.16)') // "," // &
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& json_value(mol%lattice(3, ilt) * autoaa, '(es23.16)') // "]"
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if (ilt < 3) then
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string = string // ","
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if (present(indent)) string = string // nl // indent // indent // indent
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end if
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end do
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if (present(indent)) string = string // nl // indent // indent
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string = string // "],"
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("a", indent) // json_value(cellpar(1) * autoaa, '(es23.16)') // ","
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("b", indent) // json_value(cellpar(2) * autoaa, '(es23.16)') // ","
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("c", indent) // json_value(cellpar(3) * autoaa, '(es23.16)') // ","
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("alpha", indent) // json_value(cellpar(4), '(es23.16)') // ","
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("beta", indent) // json_value(cellpar(5), '(es23.16)') // ","
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("gamma", indent) // json_value(cellpar(6), '(es23.16)') // ","
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_key("volume", indent) // json_value(volume * autoaa**3, '(es23.16)')
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if (present(indent)) string = string // nl // indent
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string = string // "}"
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end if
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string = string // ","
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if (present(indent)) string = string // nl // indent
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string = string // json_key("properties", indent) // "{}"
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if (present(indent)) string = string // nl
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string = string // "}"
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end function json_string
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pure function json_array_int_1(array, indent) result(string)
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integer, intent(in) :: array(:)
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character(len=*), intent(in), optional :: indent
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character(len=:), allocatable :: string
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integer :: i
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string = "["
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do i = 1, size(array)
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_value(array(i))
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if (i /= size(array)) string = string // ","
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end do
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if (present(indent)) string = string // nl // indent
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string = string // "]"
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end function json_array_int_1
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pure function json_array_real_1(array, indent, indent2, group) result(string)
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real(wp), intent(in) :: array(:)
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character(len=*), intent(in), optional :: indent
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character(len=*), intent(in), optional :: indent2
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integer, intent(in), optional :: group
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character(len=:), allocatable :: string
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integer :: i, j, step
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step = 1
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if (present(group)) step = group
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string = "["
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do i = 1, size(array), step
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if (present(indent2)) then
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string = string // nl // indent2
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else if (present(indent)) then
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string = string // nl // indent // indent
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end if
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do j = 1, step, 1
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string = string // json_value(array(i + j - 1), '(es23.16)')
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if (i + j - 1 /= size(array)) string = string // ","
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end do
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end do
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if (present(indent)) string = string // nl // indent
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string = string // "]"
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end function json_array_real_1
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pure function json_array_char_1(array, indent) result(string)
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character(len=*), intent(in) :: array(:)
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character(len=*), intent(in), optional :: indent
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character(len=:), allocatable :: string
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integer :: i
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string = "["
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do i = 1, size(array)
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if (present(indent)) string = string // nl // indent // indent
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string = string // json_value(trim(array(i)))
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if (i /= size(array)) string = string // ","
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end do
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if (present(indent)) string = string // nl // indent
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string = string // "]"
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end function json_array_char_1
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pure function json_key(key, indent) result(string)
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character(len=*), intent(in) :: key
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character(len=*), intent(in), optional :: indent
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character(len=:), allocatable :: string
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if (present(indent)) then
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string = json_value(key) // ": "
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else
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string = json_value(key) // ":"
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end if
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end function json_key
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pure function json_value_char(val) result(string)
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character(len=*), intent(in) :: val
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character(len=:), allocatable :: string
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string = """" // val // """"
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end function json_value_char
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pure function json_value_real(val, format) result(str)
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real(wp), intent(in) :: val
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character(len=*), intent(in) :: format
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character(len=:), allocatable :: str
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character(len=128) :: buffer
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integer :: stat
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write(buffer, format, iostat=stat) val
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if (stat == 0) then
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str = trim(buffer)
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else
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str = """*"""
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end if
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end function json_value_real
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pure function json_value_int(val) result(string)
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integer, intent(in) :: val
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character(len=:), allocatable :: string
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integer, parameter :: buffer_len = range(val)+2
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character(len=buffer_len) :: buffer
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integer :: pos
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integer :: n
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character(len=1), parameter :: numbers(0:9) = &
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["0", "1", "2", "3", "4", "5", "6", "7", "8", "9"]
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if (val == 0) then
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string = numbers(0)
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return
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end if
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n = abs(val)
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buffer = ""
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pos = buffer_len + 1
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do while (n > 0)
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pos = pos - 1
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buffer(pos:pos) = numbers(mod(n, 10))
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n = n/10
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end do
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if (val < 0) then
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pos = pos - 1
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buffer(pos:pos) = '-'
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end if
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string = buffer(pos:)
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end function json_value_int
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!> Convert direct lattice to cell parameters
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pure subroutine dlat_to_cell(lattice,cellpar)
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implicit none
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real(wp),intent(in) :: lattice(3,3) !< direct lattice
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real(wp),intent(out) :: cellpar(6) !< cell parameters
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associate( alen => cellpar(1), blen => cellpar(2), clen => cellpar(3), &
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& alp => cellpar(4), bet => cellpar(5), gam => cellpar(6) )
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alen = norm2(lattice(:,1))
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blen = norm2(lattice(:,2))
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clen = norm2(lattice(:,3))
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alp = acos(dot_product(lattice(:,2),lattice(:,3))/(blen*clen))
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bet = acos(dot_product(lattice(:,1),lattice(:,3))/(alen*clen))
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gam = acos(dot_product(lattice(:,1),lattice(:,2))/(alen*blen))
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end associate
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end subroutine dlat_to_cell
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end module mctc_io_write_pymatgen
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