Release 3.0.0

.VERSION

@@ -1 +1 @@
-2.6.1
+3.0.0

CMakeLists.txt

@@ -1,19 +1,35 @@
-cmake_minimum_required ( VERSION 2.8.8 )
+# This file is part of xslib
+# https://github.com/JureCerar/xslib
+#
+# Copyright (C) 2019-2022 Jure Cerar
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+cmake_minimum_required ( VERSION 2.9 )
 project ( xslib LANGUAGES C Fortran )
 
-# Add /cmake subdirectory
+# Add Cmake subdirectory and call packages.
 list ( APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" )
-
-# Set project find packages, define Compiler flags, set Version, and make Public.
 include ( FindPackages )
-include ( SetCompilerFlags )
-include ( SetVersion )
+include ( CompilerSettings )
+include ( Version )
 include ( Info )
 include ( Public )
 
-# Main build script
+# Add main build script
 add_subdirectory ( src )
 
-# Tests
+# Add testing script
 enable_testing ()
-add_subdirectory ( examples )
+add_subdirectory ( tests )

README.md

@@ -1,108 +1,80 @@
-# xslib - Extra-Small Library
-
-[![Version](https://img.shields.io/badge/Version-v2.6.0-blue.svg)](https://github.com/JureCerar/xslib/releases)
-![Language](https://img.shields.io/badge/Language-Fortran,_C-brightgreen.svg)
-[![License](https://img.shields.io/badge/License-GNU_GPL_v3.0-red.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
-
-<!--
-NOTE: Old dynamic badge for package version.
-[![GitHub version](https://img.shields.io/github/release/JureCerar/xslib.svg?label=Version&color=blue)](https://github.com/JureCerar/xslib/releases)
-Generic badge:
-[![Generic badge](https://img.shields.io/badge/<SUBJECT>-<STATUS>-<COLOR>.svg)](https://shields.io/)
--->
-
-The Extra-Small Library (xslib) is a modern Fortran library consisting of useful utilities and functions that "computer chemist" might need during his/her work. It uses an object-oriented philosophy for reading and storing data for analysis. The library is written with primary purpose of learning modern Fortran language, good coding practices, and in hopes that it helps someone else in their pursuit of knowledge.
-
-The library features functions to handle different molecular file types:
-- [.xyz](https://en.wikipedia.org/wiki/XYZ_file_format) - Simple *"name,x,y,z"* file that gets the job done in most cases,
-- [.gro](http://manual.gromacs.org/archive/5.0.3/online/gro.html) - GROMACS coordinate file,  
-- [.pdb](https://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html) - Protein Data Bank which is most commonly used and widely spread molecular coordinate file,
-- [.xtc](http://manual.gromacs.org/archive/5.0.3/online/xtc.html) - GROMACS compressed binary trajectory files,
-- [.trr](hhttp://manual.gromacs.org/archive/5.0.3/online/trr.html) - GROMACS binary trajectory files containing coordinates/velocities/forces,
-- [.dcd](https://www.ks.uiuc.edu/Research/namd/2.9/ug/node11.html) - Single precision binary trajectory used by NAMD, CHARMM and LAMMPS,
-- [.cub](https://h5cube-spec.readthedocs.io/en/latest/cubeformat.html) - Gaussian CUBE file format,
-
-supporting file types:
-- [.ndx](http://manual.gromacs.org/archive/5.0.3/online/ndx.html) - GROMACS index file containing user defined sets of atoms,
-- [.tpl]() - Our own proprietary file type with condensed configuration information,
-
-and data file types
-- [.pdh](http://goldenberg.biology.utah.edu/downloads/usTooDocs_Sept2012.pdf) - Standard format for storing Small-Angle X-Ray Scattering (SAXS) data.
-- [.csv](https://en.wikipedia.org/wiki/Comma-separated_values) - Comma-separated value files.
-
-## Build & Install
-Clone or download repository from GitHub:
-```bash
-git clone https://github.com/JureCerar/xslib
-```
-Move into directory and type the following:
-```bash
-mkdir build
-cd build
-cmake ..
-make
-make check
-```
-To install library type the following as *root* (or *sudo*):
-```bash
-make install
-```
-You should consider using the following [CMake options](https://cmake.org/cmake/help/v3.6/manual/cmake.1.html) with the appropriate value instead of `xxx`:
-- `-DCMAKE_Fortran_COMPILER=xxx` equal to the name of the Fortran Compiler you wish to use (or the ENV variable `FC`)
-- `-DCMAKE_C_COMPILER=xxx` equal to the name of the C Compiler you wish to use (or the ENV variable `CC`)
-- `-DCMAKE_INSTALL_PREFIX=xxx` to install xslib to a non-standard location (default `/usr/local/lib/`)  
-- `-DCMAKE_BUILD_TYPE=xxx` equal to `RELEASE` for normal build or `DEBUG` for debugging purposes.
-
-## Usage
-On how to interface with the xslib library, please read [API documentation](doc/API.md) below.  
-To use the library put `use xslib` in the module section of your program:
-```fortran
-program main
-  use xslib
-  implicit none
-  ! ...
-end program main
-```
-When compiling your program add `-lxslib` flag. You may also need to use `-I` flag to point to where the modules files are (default *-I/usr/local/include*) even with all of the right environment variables set. When linking use `-L` to point to library file (default *-L/usr/local/lib*).
-
-To make things easier **pkg-config** file is also included to help you with your program compilation. You may need to add the config file to `PKG_CONFIG_PATH` environment variable (default */usr/local/lib/pkgconfig*).
-```bash
-pkg-config xslib --libs --cflags
-```
-
-Alternatively, the library can be added via **CMake**:
-```cmake
-# Find xslib package
-find_package ( xslib 2.0.0 REQUIRED )
-include_directories ( ${xslib_INCLUDE_DIRS} )
-
-...
-
-# link (shared) xslib library
-target_link_libraries ( ${CMAKE_PROJECT_NAME} ${xslib_LIBRARIES} )
-
-# or link STATIC xslib library
-target_link_libraries ( ${CMAKE_PROJECT_NAME} ${xslib_STATIC_LIBRARIES} )
-```
-**NOTE:** In case of non-standard installation path use the following CMake option (with the appropriate value instead of `xxx`):
-- `-Dxslib_DIR=xxx` equal to path to `xslib-config.cmake` (default is */usr/local/lib/cmake/xslib-X.X.X/* ).
-
-## [API documentation](doc/README.md)
-
-## [Changelog](doc/CHANGELOG.md)
-
-## Acknowledgments
-This library includes modified versions of [libxdrfile](https://github.com/wesbarnett/libxdrfile) and its Fortran wrapper [libgmxfort](https://github.com/wesbarnett/libgmxfort) for reading GROMACS .ndx, .trr, and .xtc files created by [James W. Barnett](https://github.com/wesbarnett).
-
-<!-- Basically, he is my hero. -->
-
-## License
-This program is licensed under the **GNU General Public License v3.0**
-
-Copyright (C) 2019-2020 [Jure Cerar](https://github.com/JureCerar)
-
-This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
+# xslib - Extra-Small Library
+
+[![Release](https://img.shields.io/github/release/JureCerar/xslib.svg?label=Release&color=blue)](https://github.com/JureCerar/xslib/releases)
+![Language](https://img.shields.io/badge/Language-Fortran,_C-brightgreen.svg)
+[![License](https://img.shields.io/badge/License-GNU_GPL_v3.0-red.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
+
+The Extra-Small Library (xslib) is a modern Fortran library consisting of useful utilities and functions as stand-in for Fortran "standard" library. The library is written with primary purpose of learning modern Fortran language, good coding practices, and in hopes that it helps someone else on their quest of learning Fortran.
+
+## Build & Install
+For latest build clone repository from GitHub (or download other [releases](https://github.com/JureCerar/xslib/releases)):
+```bash
+git clone https://github.com/JureCerar/xslib
+```
+Move into directory and type the following:
+```bash
+mkdir build
+cd build
+cmake ..
+make
+make test
+```
+To install the library type the following as *root* (or *sudo*):
+```bash
+make install
+```
+You should consider using the following [CMake options](https://cmake.org/cmake/help/v3.6/manual/cmake.1.html) with the appropriate value instead of `xxx`:
+- `-DCMAKE_Fortran_COMPILER=xxx` equal to the Fortran compiler (or use ENV variable `FC`)
+- `-DCMAKE_C_COMPILER=xxx` equal to the C compiler (or use ENV variable `CC`)
+- `-DCMAKE_INSTALL_PREFIX=xxx` to install xslib to a non-standard location (default `/usr/local/lib/`)  
+- `-DCMAKE_BUILD_TYPE=xxx` equal to `RELEASE` for normal build or `DEBUG` for debugging purposes.
+
+## Documentation
+Documentation is a work in progress and is available [here](doc/README.md).  
+
+## Usage
+To use the library in your project add `use xslib` in the modules section of your program:
+```fortran
+program main
+  use xslib
+  implicit none
+  ! ...
+end program main
+```
+When compiling your program add `-lxslib` flag to compiler otions. You may also need to use `-I` flag to point to where the modules files are (default `-I/usr/local/include`) even with all of the right environment variables set. When linking use `-L` to point to library file (default `-L/usr/local/lib`).
+
+To make things easier **pkg-config** file is also included to help you with your program compilation. You may need to add the config file to `PKG_CONFIG_PATH` environment variable (default '/usr/local/lib/pkgconfig').
+```bash
+pkg-config xslib --libs --cflags
+```
+
+Alternatively, the library can be added with [CMake](https://cmake.org/). First, find the library on your computer::
+```cmake
+find_package ( xslib 3.0 REQUIRED )
+include_directories ( ${xslib_INCLUDE_DIRS} )
+```
+Then link *shared* or *static* library to your target build:
+```cmake
+# Link shared library
+target_link_libraries ( ${CMAKE_PROJECT_NAME} ${xslib_LIBRARIES} )
+# OR link static library
+target_link_libraries ( ${CMAKE_PROJECT_NAME} ${xslib_STATIC_LIBRARIES} )
+```
+**NOTE:** In case of non-standard installation path use the following CMake option (with the appropriate value instead of `xxx`):
+- `-Dxslib_DIR=xxx` equal to CMake config file path (default is `/usr/local/lib/cmake/xslib-X.X.X`).
+
+## Notes
+Functions for handling molecular files is now available seperatly. See [`atomlib`](https://github.com/JureCerar/atom) for more information.
+
+Also check out (arguably *much* better) [Fortran-lang/stdlib](https://github.com/fortran-lang/stdlib) project.
+
+## License
+This program is licensed under the **GNU General Public License v3.0**
+
+Copyright (C) 2019-2022 [Jure Cerar](https://github.com/JureCerar)
+
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

cmake/CompilerSettings.cmake

@@ -0,0 +1,47 @@
+# This file is part of xslib
+# https://github.com/JureCerar/xslib
+#
+# Copyright (C) 2019-2022 Jure Cerar
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# Set `RELEASE` as default build type
+if ( NOT CMAKE_BUILD_TYPE )
+  set ( CMAKE_BUILD_TYPE "RELEASE" CACHE STRING "Build configuration 'RELEASE' or 'DEBUG'." FORCE )
+  message ( STATUS "CMAKE_BUILD_TYPE not given, defaulting to RELEASE.")
+else ()
+  message ( STATUS "CMAKE_BUILD_TYPE is: ${CMAKE_BUILD_TYPE}")
+endif ()
+
+# Fortran compiler settings
+if ( ${CMAKE_Fortran_COMPILER_ID} STREQUAL "GNU" )
+  set ( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -march=native" )
+  set ( CMAKE_Fortran_FLAGS_RELEASE "-O3 -ffast-math -flto -fexcess-precision=fast -funroll-loops" )
+  set ( CMAKE_Fortran_FLAGS_DEBUG "-g -Og -Wall -fcheck=all -fbacktrace" )
+else ()
+  set ( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -march=native" )
+  set ( CMAKE_Fortran_FLAGS_RELEASE "-O3" )
+  set ( CMAKE_Fortran_FLAGS_DEBUG "-g -Og" )  
+endif ()
+
+# C compiler settings
+if ( ${CMAKE_C_COMPILER_ID} STREQUAL "GNU" )
+  set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native" )
+  set ( CMAKE_C_FLAGS_RELEASE "-O3 -ffast-math -flto -fexcess-precision=fast -funroll-loops" )
+  set ( CMAKE_C_FLAGS_DEBUG "-g -Og -Wall" )
+else ()
+  set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native" )
+  set ( CMAKE_C_FLAGS_RELEASE "-O3" )
+  set ( CMAKE_C_FLAGS_DEBUG "-g -Og" )
+endif ()

cmake/FindPackages.cmake

@@ -1,7 +1,23 @@
-## Required packages
+# This file is part of xslib
+# https://github.com/JureCerar/xslib
+#
+# Copyright (C) 2019-2022 Jure Cerar
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-# OpenMP library
-find_package( OpenMP )
+# Find OpenMP library 
+find_package ( OpenMP )
 if ( OpenMP_FOUND )
   list ( APPEND CMAKE_Fortran_FLAGS ${OpenMP_Fortran_FLAGS} )
   list ( APPEND CMAKE_C_FLAGS ${OpenMP_C_FLAGS} )

cmake/Info.cmake

@@ -1,5 +1,23 @@
+# This file is part of xslib
+# https://github.com/JureCerar/xslib
+#
+# Copyright (C) 2019-2022 Jure Cerar
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 # Set PKG-CONFIG package information
-set ( PROJECT_DESCRIPTION "Fortran library with useful I/O utilities and functions." )
+set ( PROJECT_DESCRIPTION "Fortran library with useful utilities and functions." )
 set ( PROJECT_URL "https://github.com/JureCerar/xslib" )
 set ( LIBDIR "lib" )
 set ( INCLUDEDIR "include/${CMAKE_PROJECT_NAME}" )