To build this project from the source code in this repository you need to have a Fortran compiler supporting Fortran 2008 and one of the supported build systems:
- meson version 0.55 or newer, with a build-system backend, i.e. ninja version 1.7 or newer
- cmake version 3.14 or newer, with a build-system backend, i.e. ninja version 1.10 or newer
- fpm version 0.3.0 or newer
Currently this project supports GCC, Intel and PGI/NVHPC compilers.
Setup a build with
meson setup _build
You can select the Fortran compiler by the FC
environment variable.
To compile the project run
meson compile -C _build
You can run the projects testsuite with
meson test -C _build --print-errorlogs
To include mctc-lib
in your project add the following wrap file to your subprojects directory:
[wrap-git]
directory = mctc-lib
url = https://github.com/grimme-lab/mctc-lib
revision = head
You can retrieve the dependency from the wrap fallback with
mctc_dep = dependency('mctc-lib', fallback: ['mctc-lib', 'mctc_dep'])
and add it as dependency to your targets.
Alternatively, this project can be build with CMake (in this case ninja 1.10 or newer is required):
cmake -B _build -G Ninja
To compile the project with CMake run
cmake --build _build
You can run the project testsuite with
pushd _build && ctest && popd
To include mctc-lib
in your CMake project retrieve it using the FetchContent
module:
if(NOT TARGET mctc-lib)
set("mctc-lib-url" "https://github.com/grimme-lab/mctc-lib")
message(STATUS "Retrieving mctc-lib from ${mctc-lib-url}")
include(FetchContent)
FetchContent_Declare(
"mctc-lib"
GIT_REPOSITORY "${mctc-lib-url}"
GIT_TAG "HEAD"
)
FetchContent_MakeAvailable("mctc-lib")
endif()
And link against the "mctc-lib"
interface library.
target_link_libraries("${PROJECT_NAME}-lib" PUBLIC "mctc-lib")
Invoke fpm in the project root with
fpm build
To run the testsuite use
fpm test
You can access the mctc-convert
program using the run subcommand
fpm run -- --help
To use mctc-lib
for testing include it as dependency in your package manifest
[dependencies]
mctc-lib.git = "https://github.com/grimme-lab/mctc-lib"
An example application is provided with the mctc-convert
program to convert between different supported input formats.
To read an input file using the IO library use the read_structure
routine.
The final geometry data is stored in a structure_type
:
use mctc_io
use mctc_env
type(structure_type) :: mol
type(error_type), allocatable :: error
call read_structure(mol, "input.xyz", error)
if (allocated(error)) then
print '(a)', error%message
error stop
end if
The environment library provides a basic error back-propagation mechanism using an allocatable error_type
, which is passed to the library routines.
Usually the reader can detect the file type from the suffix of file names.
Alternatively, the filetype
enumerator provides the identifiers of all supported file types, which can be passed as optional argument to the read_structure
routine.
In a similar way the write_structure
routine allows to write a structure_type
to a file or unit:
use mctc_io
use mctc_env
type(structure_type) :: mol
type(error_type), allocatable :: error
call write_structure(mol, "output.xyz", error)
if (allocated(error)) then
print '(a)', error%message
error stop
end if
The mctc-convert
program provides a chained reader and writer call to act as a geometry file converter.
Checkout the implementation in app/main.f90
.
The geometry input readers try to be provide helpful error messages, no user should be left alone with an error message like invalid input. Unclear error messages are considered a bug in mctc-lib, if you struggle to make sense of a reported error, file us an issue and we will make the report better.
How can helpful error messages look like? Here are some examples.
- negative number of atoms declared in xyz file
Error: Impossible number of atoms provided
--> struc.xyz:1:1-2
|
1 | -3
| ^^ expected positive integer value
|
- total charge is not specified as integer
Error: Cannot read eht entry
--> struc.coord:18:13-15
|
18 | $eht charge=one unpaired=0
| ^^^ expected integer value
|
- a fixed width entry contains an incorrect value
Error: Cannot read charges
--> struc.mol:29:23-25
|
29 | M CHG 3 1 1 3 b 2 -1
| ^^^ expected integer value
|
- Turbomole input with confliciting data groups
Error: Conflicting lattice and cell groups
--> struc.coord:37:1-5
|
35 | $lattice angs
| -------- lattice first defined here
:
37 | $cell angs
| ^^^^^ conflicting cell group
|
We try to retain as much information as possible when displaying the error message to make it easy to fix the offending part in the input.
Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “as is” basis, without warranties or conditions of any kind, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this project by you, as defined in the Apache-2.0 license, shall be licensed as above, without any additional terms or conditions.