~etsf-io-developers/etsf-io/1.0 : revision 94

1

<?xml version="1.0" encoding="ISO-8859-1"?>

2

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"

3

"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">

4

5

<head>

6

7

8

9

<title>./src/tutorials/convert_to_xyz.f90</title>

10

11

12

</head>

13

<body>

14

15

<a name="robo_top_of_doc">ETSF_IO library - documentation pages</a>

16

</div>

17

18

</div>

19

20

<h3>TABLE OF CONTENTS</h3>

21

<ul>

22

<li><a href="#robo4">convert_to_xyz</a></li>

23

</ul>

24

<hr />

25

26

</a><a name="robo4"></a><h2>convert_to_xyz</h2>

27

28

[ <a href="#robo_top_of_doc">Top</a> ] [ <a href="./README_f90.html#robo119">etsf_io_tutorials</a> ] [ <a href="../robo_tuto_cat.html#robo_top_of_doc">Tutorials</a> ]

29

NAME

30

convert_to_xyz

31

32

FUNCTION

33

In this example, we will describe how to use the high level routines from

34

<a href="../utils/etsf_io_file_f90.html#robo1">etsf_io_file</a> and <a href="../utils/etsf_io_tools_f90.html#robo3">etsf_io_tools</a> (from library etsf_io_utils). Doing it, we will

35

read a cristallographic file, check its validity and convert it to XYZ file,

36

reading the coordinates of atoms and getting their names.

37

38

39

To compile this exemple, use (assuming default installation paths):

40

41

<pre> ${F90} -I/opt/include/${F90} -o convert_to_xyz <a href="#robo_top_of_doc">convert_to_xyz.f90</a>

42

-L/opt/lib -letsf_io_utils -letsf_io -L/usr/lib -lnetcdf

43

</pre>

44

45

SOURCE

46

<pre class="source">program convert_to_xyz

47

48

use <a href="../low_level/etsf_io_low_level_f90.html#robo2">etsf_io_low_level</a>

49

use <a href="../group_level/etsf_io_f90.html#robo0">etsf_io</a>

50

use <a href="../utils/etsf_io_file_f90.html#robo1">etsf_io_file</a>

51

use <a href="../utils/etsf_io_tools_f90.html#robo3">etsf_io_tools</a>

52

53

implicit none

54

55

integer :: iargc

56

character(len = <a href="../low_level/public_variables_f90.html#robo71">etsf_io_low_error_len</a>) :: filename, error_string

57

logical :: lstat

58

type(<a href="../low_level/public_variables_f90.html#robo68">etsf_io_low_error</a>) :: error_data

59

integer :: i_atom

60

double precision :: coord(etsf_3dimlen)

61

</pre>

62

NOTES

63

In this tutorial, we will open an ETSF file, and some variable of the

64

geometry group (see the first tutorial on how to <a href="./create_a_crystal_den_file_f90.html#robo5">create_a_crystal_den_file</a>

65

for further explanations on groups and especially <a href="../group_level/etsf_io_f90.html#robo12">etsf_geometry</a>).

66

67

68

The required data to create an XYZ file are:

69

70

<ul><li> primitive_vectors for the box definition,

71

</li>

72

<li> reduced_atom_positions for the atom coordinates,

73

</li>

74

<li> atom_species for the nature of elements.

75

</li>

76

</ul>

77

78

SOURCE

79

<pre class="source"> integer :: ncid

80

type(<a href="../group_level/etsf_io_f90.html#robo10">etsf_dims</a>) :: dims_data

81

type(<a href="../group_level/etsf_io_f90.html#robo12">etsf_geometry</a>) :: geometry_data

82

double precision, allocatable, target :: primitive_vectors(:,:)

83

double precision, allocatable, target :: reduced_atom_positions(:,:)

84

integer, allocatable, target :: atom_species(:)

85

</pre>

86

NOTES

87

The names of atoms receives a special treatment since it can be found in several

88

variables. The specifications are clear on preference and we will use the

89

<a href="../utils/etsf_io_tools_f90.html#robo116">etsf_io_tools_get_atom_names</a>() routine to handle this preference and read

90

the atom names.

91

92

SOURCE

93

<pre class="source"> character(len = etsf_charlen), allocatable :: atom_names(:)

94

</pre>

95

NOTES

96

We read the number of argument and get the input filename from the command line.

97

98

SOURCE

99

<pre class="source"> ! Read number of program argument, should be one.

100

if (iargc() /= 1) then

101

write(0, *) "Error: one argument is required."

102

stop

103

end if

104

! Read name of input file.

105

call getarg(1, filename)

106

</pre>

107

NOTES

108

Before doing anything else, we check that our file is a valid crystallographic

109

file. To do it, we use the module <a href="../utils/etsf_io_file_f90.html#robo1">etsf_io_file</a> and its routine

110

<a href="../utils/etsf_io_file_public_f90.html#robo41">etsf_io_file_check</a>(). This routine will open the given file and check that it

111

machtes one or several requirements (see flags in <a href="../group_level/etsf_io_f90.html#robo120">ETSF_IO_VALIDITY_FLAGS</a>). Flags

112

can be added to form a complex validation on several specifications.

113

114

115

If an error occurs, we transform the error data to a string and output it on

116

the standard error.

117

118

SOURCE

119

<pre class="source"> call <a href="../utils/etsf_io_file_public_f90.html#robo41">etsf_io_file_check</a>(trim(filename), etsf_crystallographic_data, &

120

& lstat, error_data)

121

if (.not. lstat) then

122

write(0, *) "Error: invalid input file, it does not match crystallographic"

123

write(0, *) " requirements. Given reason:"

124

call <a href="../low_level/etsf_io_low_level_f90.html#robo73">etsf_io_low_error_to_str</a>(error_string, error_data)

125

write(0, "(A)") trim(error_string)

126

stop

127

end if

128

</pre>

129

NOTES

130

Now that our file is valid, we will follow a step by step procedure to

131

reopen it, read the dimensions, allocate our temporary arrays, read the required

132

informations, get the atoms names, close the file and output the informations

133

in XYZ format.

134

135

SOURCE

136

<pre class="source"> call <a href="../low_level/read_routines_f90.html#robo80">etsf_io_low_open_read</a>(ncid, trim(filename), lstat, error_data = error_data)

137

if (.not. lstat) then

138

call <a href="../low_level/etsf_io_low_level_f90.html#robo73">etsf_io_low_error_to_str</a>(error_string, error_data)

139

write(0, "(A)") trim(error_string)

140

stop

141

end if

142

</pre>

143

NOTES

144

The dimensions are read and stored into dims_data.

145

146

SOURCE

147

<pre class="source"> call <a href="../group_level/etsf_io_dims_get_f90.html#robo34">etsf_io_dims_get</a>(ncid, dims_data, lstat, error_data)

148

if (.not. lstat) then

149

call <a href="../low_level/etsf_io_low_level_f90.html#robo73">etsf_io_low_error_to_str</a>(error_string, error_data)

150

write(0, "(A)") trim(error_string)

151

stop

152

end if

153

</pre>

154

NOTES

155

We allocate the local arrays where to put the read informations.

156

157

SOURCE

158

<pre class="source"> allocate(primitive_vectors(dims_data%number_of_cartesian_directions, &

159

& dims_data%number_of_vectors))

160

allocate(reduced_atom_positions(dims_data%number_of_reduced_dimensions, &

161

& dims_data%number_of_atoms))

162

allocate(atom_species(dims_data%number_of_atoms))

163

allocate(atom_names(dims_data%number_of_atom_species))

164

geometry_data%primitive_vectors => primitive_vectors

165

geometry_data%reduced_atom_positions => reduced_atom_positions

166

geometry_data%atom_species => atom_species

167

</pre>

168

NOTES

169

We get the informations from the NetCDF file for the pointers that have been

170

associated in geometry_data.

171

172

SOURCE

173

<pre class="source"> call <a href="../group_level/etsf_io_geometry_get_f90.html#robo50">etsf_io_geometry_get</a>(ncid, geometry_data, lstat, error_data)

174

if (.not. lstat) then

175

call <a href="../low_level/etsf_io_low_level_f90.html#robo73">etsf_io_low_error_to_str</a>(error_string, error_data)

176

write(0, "(A)") trim(error_string)

177

stop

178

end if

179

</pre>

180

NOTES

181

We use the high level routine that get the names of atoms. If the file is valid,

182

it always returns string informations (into @atom_names), but atomic numbers can

183

also be returned as double values in an optional array (see @atom_numbers). We

184

don't need here the double values, so we don't use the optional argument.

185

186

SOURCE

187

<pre class="source"> call <a href="../utils/etsf_io_tools_f90.html#robo116">etsf_io_tools_get_atom_names</a>(ncid, atom_names, lstat, error_data)

188

if (.not. lstat) then

189

call <a href="../low_level/etsf_io_low_level_f90.html#robo73">etsf_io_low_error_to_str</a>(error_string, error_data)

190

write(0, "(A)") trim(error_string)

191

stop

192

end if

193

</pre>

194

NOTES

195

We don't forget to close the file.

196

197

SOURCE

198

<pre class="source"> call <a href="../low_level/etsf_io_low_level_f90.html#robo64">etsf_io_low_close</a>(ncid, lstat, error_data)

199

if (.not. lstat) then

200

call <a href="../low_level/etsf_io_low_level_f90.html#robo73">etsf_io_low_error_to_str</a>(error_string, error_data)

201

write(0, "(A)") trim(error_string)

202

stop

203

end if

204

</pre>

205

NOTES

206

Finally we output informations in XYZ format.

207

208

SOURCE

209

<pre class="source"> write(*, "(I0)") dims_data%number_of_atoms

210

write(*, "(3A)") "Converted from '", trim(filename), "'"

211

do i_atom = 1, dims_data%number_of_atoms, 1

212

coord(1) = primitive_vectors(1, 1) * reduced_atom_positions(1, i_atom) + &

213

& primitive_vectors(2, 1) * reduced_atom_positions(2, i_atom) + &

214

& primitive_vectors(3, 1) * reduced_atom_positions(3, i_atom)

215

coord(2) = primitive_vectors(1, 2) * reduced_atom_positions(1, i_atom) + &

216

& primitive_vectors(2, 2) * reduced_atom_positions(2, i_atom) + &

217

& primitive_vectors(3, 2) * reduced_atom_positions(3, i_atom)

218

coord(3) = primitive_vectors(1, 3) * reduced_atom_positions(1, i_atom) + &

219

& primitive_vectors(2, 3) * reduced_atom_positions(2, i_atom) + &

220

& primitive_vectors(3, 3) * reduced_atom_positions(3, i_atom)

221

write(*, "(A,3E16.6)") trim(atom_names(atom_species(i_atom))), coord

222

end do

223

224

deallocate(primitive_vectors)

225

deallocate(reduced_atom_positions)

226

deallocate(atom_species)

227

deallocate(atom_names)

228

end program convert_to_xyz

229

</pre>

230

231

</div>

232

233

Generated from ./src/tutorials/convert_to_xyz.f90 with <a href="http://www.xs4all.nl/~rfsber/Robo/robodoc.html">ROBODoc</a> V4.99.30 on Mon Mar 29 2010 11:04:46

234

235

</div>

236

</body>

237

</html>