XYZ_IO
XYZ File Input/Output routines.

XYZ_IO is a FORTRAN90 library which reads and writes files in the XYZ, XYZL and XYZF formats.

XYZ files are a simple way of storing information about sets of points in 3D.

An XYZ file has a simple structure. There are three kinds of records:

• COMMENT LINES begin with the character '#' and are ignored;
• BLANK LINES are ignored;
• COORDINATE LINES each contain one triple of XYZ coordinates;

Here is an example of an XYZ file containing 13 points:

#  cube.xyz
#
        0.000000        0.000000        0.000000
        1.000000        0.000000        0.000000
        1.000000        1.000000        0.000000
        0.000000        1.000000        0.000000
        0.000000        0.000000        1.000000
        1.000000        0.000000        1.000000
        1.000000        1.000000        1.000000
        0.000000        1.000000        1.000000
      

Of course, in many cases, we would like to describe LINES between the points. We can add this information by including a second file, called an XYZL file, which consists of a string of point indices. A line is drawn from one point to the next, and so on, through all the points index on the record. Thus, an XYZL file associated with the above XYZ file might be:

#  cube.xyzl
#
  1 2 3 4 1
  5 6 7 8 5
  1 5
  2 6
  3 7
  4 8
      

We might also like to describe FACES defined by the points. We can add this information by including a file, called an XYZF file, which consists of a string of point indices. A face is defined by listing in counterclockwise order the vertices that lie on it. The first vertex is not repeated as the final vertex. Thus, an XYZF file associated with the above XYZ file might be:

#  cube.xyzf
#
  1 4 3 2
  2 3 7 6
  5 6 7 8
  5 8 4 1
  1 2 6 5
  3 4 8 7
      

Licensing:

The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.

Languages:

XYZ_IO is available in a C++ version and a FORTRAN90 version and a MATLAB version.

Related Data and Programs:

IVREAD, a FORTRAN90 program which can convert graphics information between various 3D formats, including the XYZ format.

PDB_TO_XYZ, a FORTRAN90 program which reads the ATOM records from a PDB file, and writes the atomic coordinates to an XYZ file.

SPHERE_VORONOI, a FORTRAN90 library which reads an XYZ file of 3D points on the unit sphere, and computes and plots Delaunay triangulations and Voronoi diagrams.

XY, a data directory which contains examples of XY files, a simple 2D graphics point and line format;

XYZ, a data directory which contains examples of XYZ files, a simple 3D graphics point and line format;

XYZ_DISPLAY, a MATLAB program which reads XYZ information defining points in 3D, and displays an image in the MATLAB graphics window.

XYZ_DISPLAY_OPENGL, a C++ program which reads an XYZ file of 3D point coordinates, and displays an image of those points using OpenGL.

XYZ_TO_PDB, a FORTRAN90 program which reads a set of XYZ spatial coordinates, and rewrites them as ATOM records in a PDB file.

XYZF, a data directory which contains examples of XYZF files, a simple 3D graphics point and face format;

XYZF_DISPLAY, a MATLAB program which reads XYZF information defining points and faces in 3D, and displays an image in a MATLAB graphics window.

XYZF_DISPLAY_OPENGL, a C++ program which reads XYZL information defining points and faces in 3D, and displays an image using OpenGL.

XYZL, a data directory which contains examples of XYZL files, a simple 3D graphics point and line format;

XYZL_DISPLAY, a MATLAB program which reads XYZL information defining points and lines in 3D, and displays an image in a MATLAB graphics window.

XYZL_DISPLAY_OPENGL, a C++ program which reads XYZL information defining points and lines in 3D, and displays an image using OpenGL.

Source Code:

• xyz_io.f90, the source code.

Examples and Tests:

• xyz_io_test.f90, a sample calling program.
• xyz_io_test.txt, the output file.
• helix.xyz, an XYZ file created by the example program.
• xy_io_prb_02.xyz, an XYZ file created by the example program.
• cube.xyz, an XYZ file of points created by the example program.
• cube.xyzl, an XYZL file of lines created by the example program.
• cube.xyzf, an XYZF file of lines created by the example program.

List of Routines:

• CH_CAP capitalizes a single character.
• CH_EQI is a case insensitive comparison of two characters for equality.
• CH_TO_DIGIT returns the integer value of a base 10 digit.
• GET_UNIT returns a free FORTRAN unit number.
• S_TO_I4 reads an integer value from a string.
• S_TO_I4VEC reads an integer vector from a string.
• S_TO_R8 reads an R8 value from a string.
• S_TO_R8VEC reads an R8VEC from a string.
• S_WORD_COUNT counts the number of "words" in a string.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• TIMESTRING writes the current YMDHMS date into a string.
• WORD_NEXT_READ "reads" words from a string, one at a time.
• XYZ_DATA_PRINT prints the data of an XYZ file.
• XYZ_DATA_READ reads data from an XYZ file.
• XYZ_DATA_WRITE writes the data of an XYZ file.
• XYZ_EXAMPLE computes points for an example XYZ dataset.
• XYZ_EXAMPLE_SIZE sizes an example XYZ dataset.
• XYZ_HEADER_PRINT prints the header of an XYZ file.
• XYZ_HEADER_READ determines the number of pairs of data in an XYZ file.
• XYZ_HEADER_WRITE writes the header of an XYZ file.
• XYZ_READ reads graphics information from an XYZ file.
• XYZ_WRITE writes an XYZ file.
• XYZ_WRITE_TEST tests the XYZ write routines.
• XYZF_DATA_PRINT prints the data of an XYZF file.
• XYZF_DATA_READ reads the data in an XYZF file.
• XYZF_DATA_WRITE writes the data of an XYZF file.
• XYZF_EXAMPLE sets data suitable for a pair of XYZ and XYZF files.
• XYZF_EXAMPLE_SIZE sizes the data to be created by XYZF_EXAMPLE.
• XYZF_HEADER_PRINT prints the header of an XYZF file.
• XYZF_HEADER_READ determines the number of face items in an XYZF file.
• XYZF_HEADER_WRITE writes the header of an XYZF file.
• XYZF_WRITE writes an XYZF file.
• XYZL_DATA_PRINT prints the data of an XYZL file.
• XYZL_DATA_READ reads the data in an XYZL file.
• XYZL_DATA_WRITE writes the data of an XYZL file.
• XYZL_EXAMPLE sets data suitable for a pair of XYZ and XYZL files.
• XYZL_EXAMPLE_SIZE sizes the data to be created by XYZL_EXAMPLE.
• XYZL_HEADER_PRINT prints the header of an XYZL file.
• XYZL_HEADER_READ determines the number of line items in an XYZL file.
• XYZL_HEADER_WRITE writes the header of an XYZL file.
• XYZL_WRITE writes an XYZL file.

You can go up one level to the FORTRAN90 source codes.