GitHub - nfaguirrec/scift: SciFT (Scientific Fortran Tools)

SciFT (Scientific Fortran Tools)

The Scientific Fortran Tools (SciFT) is a library specially oriented to scientific purposes for Fortran programmers. The library provides a wide range of mathematical routines such as random number generators, special functions, and high-level classes to manipulate strings, files parsing, matrices, grid-based numerical functions, data structures (lists, vectors, maps, graphs), and molecules.

Prerequisites

System Requirements:

SciFT is known to work on GNU/Linux. However, it should work on any POSIX-compliant system.

Dependencies:

GNU Bash
GNU Awk (gawk) (version >= 4.0)
Intel® Fortran Compiler (version >= 14.0.3)
SciFT has not been tested with any other compiler.
Intel® Math Kernel Library (Intel® MKL)
SciFT has not been tested with any other math library.

Compiling SciFT

Download the .zip file from this page and extract the files,

$ unzip scift-master.zip 
Archive:  scift-master.zip
3e330bbcb711cb2275ef1ce06aa021de764662f2
   creating: scift-master/
  inflating: scift-master/LICENSE    
  inflating: scift-master/LICENSE.FortranParser  
  inflating: scift-master/Makefile
...

$ mv scift-master scift

or clone the repository using git

$ git clone https://github.com/nfaguirrec/scift.git

The following should be the content of the scift directory if previous steps were successful:

$ cd scift
$ ls
docs      examples  LICENSE.FortranParser  README.md     src    VERSION
doxyfile  LICENSE   Makefile               SCIFTvars.sh  utils

Enter in the scift directory (cd scift) and modify the Makefile file (src/Makefile) if necessary.

To build the code just type make inside the main directory as follows:

$ source SCIFTvars.sh
$ make
Building dependencies for Atom.f90 ... OK
Building dependencies for AtomicElementsDB.f90 ... OK
Building dependencies for BlocksIFileParser.f90 ... OK
...
Building n3df.eval.f90 (0:00.79)
Building n3df.func.f90 (0:00.63)
Building n3df.oper.f90 (0:00.67)

Installing SciFT

The basic environmental variables that SciFT needs can be loaded just adding the following command anywhere in the ~/.bashrc file:

source <PATH_TO_SCIFT>/SCIFTvars.sh

Usage

The following are some examples of how to use some important classes available in SciFT

class String

The following block (test.f90) is an example of how to use the class String:

program test
	use String_

	type(String) :: str1, str2
	integer :: int1
	character(100), allocatable :: tokens(:)
	integer :: i
	
	str1 = "Hello"
	
	str2 = str1+":fortran-string"
	write(*,*) trim(str2.fstr)
	
	call str2.split( tokens, ":-" )
	do i=1,size(tokens)
		write(*,*) i, "    ", trim(tokens(i))
	end do
	
	call str2.replace( ":", " string " )
	write(*,*) trim(str2.fstr)
	
	call str2.replace( "string", "fortran", wholeWords=.true. )
	write(*,*) trim(str2.fstr)
	
	str1 = str2.toUpper()
	write(*,*) trim(str1.fstr)
end program test

It is compiled an executed as follows:

$ ifort test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift
$ ./test 
 Hello:fortran-string
           1     Hello
           2     fortran
           3     string
 Hello string fortran-string
 Hello fortran fortran-string
 HELLO FORTRAN FORTRAN-STRING

class RealList

The following block (test.f90) is an example of how to use the class List (equivalent to list< double > in C++):

program test
	use RealList_

	type(RealList) :: mylist
	class(RealListIterator), pointer :: iter
	
	call mylist.init()
	
	call mylist.append( 8.0_8 )
	call mylist.append( 5.0_8 )
	call mylist.append( 1.0_8 )
	call mylist.prepend( 0.0_8 )
	call mylist.append( [ 10.0_8, 11.0_8, 12.0_8 ] )
	
	iter => mylist.begin
	iter => iter.next
	
	call mylist.insert( iter, 3.0_8 )
	
	iter => mylist.begin
	do while( associated(iter) )
		write(*,"(A,F6.3)", advance="no") " --> ", iter.data
		
		iter => iter.next
	end do
end program test

It is compiled an executed as follows:

$ ifort test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift
$ ./test 
 -->  0.000 -->  8.000 -->  3.000 -->  5.000 -->  1.000 --> 10.000 --> 11.000 --> 12.000

class List (containing user-defined objects)

The following block (test.f90) is an example of how to specialize and use the class List to contain MyData objects. Notice that the class MyData must have defined the == operator (equivalent to list< MyData > in C++):

module MyData_
	implicit none
	private
	
	type, public :: MyData
		integer :: id
		character(2) :: name
		
		contains
			generic :: operator(==) => MyData_eq
			procedure :: MyData_eq
	end type MyData
	
	contains
	
	function MyData_eq( this, other ) result( output )
		class(MyData), intent(in) :: this, other
		logical :: output
		
		output = ( this.id == other.id .and. this.name == other.name )
	end function MyData_eq
end module MyData_

module MyList_
	use MyData_
	implicit none
	
#define List MyList
#define ListBasicInterface
#define ListIterator MyListIterator
#define __CLASS_ITEMLIST__ class(MyData)
#define __TYPE_ITEMLIST__ type(MyData)
#include "List.h90"
#undef List
#undef ListBasicInterface
#undef ListIterator
#undef __CLASS_ITEMLIST__
#undef __TYPE_ITEMLIST__

end module MyList_

program test
	use MyData_
	use MyList_
	
	type(MyList) :: list
	class(MyListIterator), pointer :: iter
	
	call list.init()
	
	call list.append( MyData(1,"a") )
	call list.append( MyData(5,"b") )
	call list.prepend( MyData(0,"c") )
	call list.append( [ MyData(0,"d"), MyData(1,"e"), MyData(2,"f") ] )
	
	iter => list.begin
	iter => iter.next
	
	call list.insert( iter, MyData(3,"g") )
	
	iter => list.begin
	do while( associated(iter) )
		write(*,"(A,I2,A3,A)", advance="no") " --> (", iter.data.id, iter.data.name, ")"
		
		iter => iter.next
	end do
end program test

It is compiled an executed as follows (notice it requires the Fortran preprocessor, -fpp):

$ ifort -fpp test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift
$ ./test 
 --> ( 0 c ) --> ( 1 a ) --> ( 3 g ) --> ( 5 b ) --> ( 0 d ) --> ( 1 e ) --> ( 2 f )

class StringIntegerMap

The following block (test.f90) is an example of how to use the class Map (equivalent to map<string, int> in C++):

program test
	use String_
	use StringIntegerPair_
	use StringIntegerMap_
	implicit none
	
	type(StringIntegerPair) :: pair
	type(StringIntegerMap) :: mymap
	class(StringIntegerMapIterator), pointer :: iter
	
	call mymap.init()
	
	call mymap.insert( String("John"), 27 )
	call mymap.insert( String("Marie"), 22 )
	call mymap.insert( String("Luna"), 24 )
	
	iter => mymap.begin
	do while( associated(iter) )
		pair = mymap.pair( iter )
		write(*,"(A15,A,I2)") pair.first.fstr, " --> ", pair.second
		
		iter => iter.next
	end do
end program test

It is compiled an executed as follows:

$ ifort test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift
$ ./test 
           John --> 27
           Luna --> 24
          Marie --> 22

class Map (containing user-defined objects)

The following block (test.f90) is an example of how to specialize and use the class Map to contain String keys and MyData values. Notice that the class MyData must have defined the == operator (equivalent to map< string, MyData > in C++):

module MyData_
	implicit none
	private
	
	type, public :: MyData
		integer :: id
		character(2) :: name
		
		contains
			generic :: operator(==) => MyData_eq
			procedure :: MyData_eq
	end type MyData
	
	contains
	
	function MyData_eq( this, other ) result( output )
		class(MyData), intent(in) :: this, other
		logical :: output
		
		output = ( this.id == other.id .and. this.name == other.name )
	end function MyData_eq
end module MyData_

module MyPair_
	use String_
	use MyData_
	implicit none
	private
	
#define Pair MyPair
#define PairBasicInterface
#define __CLASS_ITEMFIRST__ class(String)
#define __TYPE_ITEMFIRST__  type(String)
#define __CLASS_ITEMSECOND__ class(MyData)
#define __TYPE_ITEMSECOND__  type(MyData)
#define __ADD_ATTRIBUTES__
#define __ADD_METHODS__
#include "Pair.h90"
#undef Pair
#undef PairBasicInterface
#undef __CLASS_ITEMFIRST__
#undef __TYPE_ITEMFIRST__
#undef __CLASS_ITEMSECOND__
#undef __TYPE_ITEMSECOND__
#undef __ADD_ATTRIBUTES__
#undef __ADD_METHODS__
	
end module MyPair_

module MyPairList_
	use String_
	use MyPair_
	implicit none
	private
	
#define List MyPairList
#define ListBasicInterface
#define ListIterator MyPairListIterator
#define __CLASS_ITEMLIST__ class(MyPair)
#define __TYPE_ITEMLIST__ type(MyPair)
#include "List.h90"
#undef List
#undef ListBasicInterface
#undef ListIterator
#undef __CLASS_ITEMLIST__
#undef __TYPE_ITEMLIST__

end module MyPairList_

module MyMap_
	use IOStream_
	use String_
	use MyData_
	use MyPair_
	use MyPairList_, MyMapIterator => MyPairListIterator
	implicit none
	private
	
	public :: MyMapIterator
	
#define Map MyMap
#define MapBasicInterface
#define __CLASS_MAPITERATOR__  class(MyMapIterator)
#define __TYPE_MAPLIST__       type(MyPairList)
#define __TYPE_MAPPAIR__       type(MyPair)
#define __CLASS_MAPPAIR__      class(MyPair)
#define __CLASS_MAPVALUE__     class(MyData)
#define __TYPE_MAPVALUE__     type(MyData)
#define __ADD_METHODS__
#include "Map.h90"
#undef Map
#undef MapBasicInterface
#undef __CLASS_MAPITERATOR__
#undef __TYPE_MAPLIST__
#undef __TYPE_MAPPAIR__
#undef __CLASS_MAPPAIR__
#undef __CLASS_MAPVALUE__
#undef __TYPE_MAPVALUE__
#undef __ADD_METHODS__
	
end module MyMap_

program test
	use String_
	use MyData_
	use MyPair_
	use MyPairList_
	use MyMap_
	
	type(MyMap) :: mmap
	class(MyMapIterator), pointer :: iter
	type(MyPair) :: pair
	
	call mmap.init()
	
	call mmap.insert( String("John"),  MyData(1,"a") )
	call mmap.insert( String("Marie"), MyData(2,"b") )
	call mmap.insert( String("Luna"),  MyData(3,"c") )
	
	iter => mmap.begin
	do while( associated(iter) )
			pair = mmap.pair( iter )
			write(*,"(A15,A,I2,A3,A)") pair.first.fstr, &
				" --> (", pair.second.id, pair.second.name, ")"
				
			iter => iter.next
	end do
end program test

It is compiled an executed as follows (notice it requires the Fortran preprocessor, -fpp):

$ ifort -fpp test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift
$ ./test 
           John --> ( 1 a )
           Luna --> ( 3 c )
          Marie --> ( 2 b )

class IntegerGraph

The following block (test.f90) is an example of how to use the class Graph (equivalent to GTL:graph in C++):

program test
	use IntegerGraph_
	
	type(IntegerGraph) :: mygraph
	call mygraph.init( directed=.false. )
	
	!        (1)    
	!         |     
	!        (2)    
	!       /   \   
	!     (3)   (4) 
	!       \   /   
	!        (5)
	
	call mygraph.newNodes( 5 )
	
	call mygraph.newEdges( 1, [2] )
	call mygraph.newEdges( 2, [1,3,4] )
	call mygraph.newEdges( 3, [2,5] )
	call mygraph.newEdges( 4, [2,5] )
	call mygraph.newEdges( 5, [3,4] )
	
	call mygraph.computeDijkstraPaths( 1 )
	write(*,*) "distance from 1 to 5 = ", mygraph.distance(5)
end program test

It is compiled an executed as follows (notice it requires the MKL library):

$ ifort test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift -mkl
$ ./test 
 distance from 1 to 5 =    3.00000000000000

class Molecule

The following block (test.f90) is an example of how to use the class Molecule. It creates a hydrogen molecule, rotates it, and then show it on screen in the XYZ format:

program test
	use UnitsConverter_
	use Atom_
	use Molecule_
	implicit none
	
	type(Atom) :: atm
	type(Molecule) :: mol
	
	call mol.init( 2, name="Hydrogen molecule" )
	call atm.init( "H", 0.0_8, 0.0_8, 0.3561_8*angs ); mol.atoms(1) = atm
	call atm.init( "H", 0.0_8, 0.0_8,-0.3561_8*angs ); mol.atoms(2) = atm
	
	call mol.rotate( alpha=45.0*deg, beta=45.0*deg, gamma=0.0*deg )
	
	call mol.save()
end program test

It is compiled and executed as follows (notice it requires the MKL library):

$ ifort test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift -mkl
$ ./test 
           2
Hydrogen molecule
  H            0.17805000         -0.25180072          0.17805000
  H           -0.17805000          0.25180072         -0.17805000

class Matrix

The following block (test.f90) is an example of how to use the class Matrix. It creates the matrix, diagonalizes it, and then show the results in a nice format.

program test
	use Matrix_
	implicit none
	
	type(Matrix) :: A, B, C
	
	call A.init(5,5)
	A.data(1,:) = [  1.96,  -6.49,  -0.47,  -7.20,  -0.65 ]
	A.data(2,:) = [ -6.49,   3.80,  -6.39,   1.50,  -6.34 ]
	A.data(3,:) = [ -0.47,  -6.39,   4.17,  -1.51,   2.67 ]
	A.data(4,:) = [ -7.20,   1.50,  -1.51,   5.70,   1.80 ]
	A.data(5,:) = [ -0.65,  -6.34,   2.67,   1.80,  -7.10 ]
	
	write(*,*) ""
	write(*,*) "A ="
	call A.show( formatted=.true. )
	
	call A.eigen( eVecs=B, eVals=C )
	
	write(*,*) ""
	write(*,*) "eigenvectors ="
	call B.show( formatted=.true. )
	
	write(*,*) ""
	write(*,*) "eigenvalues ="
	call C.show( formatted=.true. )
end program test

It is compiled and executed as follows (notice it requires the MKL library):

$ ifort test.f90 -o test -I${SCIFT_HOME}/src -L${SCIFT_HOME}/src -lscift -mkl
$ ./test 
 
 A =
                1           2           3           4           5
    1    1.960000   -6.490000   -0.470000   -7.200000   -0.650000
    2   -6.490000    3.800000   -6.390000    1.500000   -6.340000
    3   -0.470000   -6.390000    4.170000   -1.510000    2.670000
    4   -7.200000    1.500000   -1.510000    5.700000    1.800000
    5   -0.650000   -6.340000    2.670000    1.800000   -7.100000
 
 eigenvectors =
                1           2           3           4           5
    1   -0.298067   -0.607513   -0.402620   -0.374481    0.489637
    2   -0.507798   -0.287968    0.406586   -0.357169   -0.605255
    3   -0.081606   -0.384320    0.659966    0.500764    0.399148
    4   -0.003589   -0.446730   -0.455290    0.620365   -0.456375
    5   -0.804130    0.448032   -0.172458    0.310768    0.162248
 
 eigenvalues =
                 1            2            3            4            5
    1   -11.065575     0.000000     0.000000     0.000000     0.000000
    2     0.000000    -6.228747     0.000000     0.000000     0.000000
    3     0.000000     0.000000     0.864028     0.000000     0.000000
    4     0.000000     0.000000     0.000000     8.865457     0.000000
    5     0.000000     0.000000     0.000000     0.000000    16.094837

Authors

Nestor F. Aguirre ( [email protected] )

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Name		Name	Last commit message	Last commit date
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doc		doc
examples		examples
src		src
utils		utils
LICENSE		LICENSE
LICENSE.FortranParser		LICENSE.FortranParser
Makefile		Makefile
README.md		README.md
SCIFTvars.sh		SCIFTvars.sh
VERSION		VERSION
doxyfile		doxyfile

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