~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/read_write_sub_access.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="#robo132">read_write_sub_access</a></li>

23

</ul>

24

<hr />

25

26

</a><a name="robo132"></a><h2>read_write_sub_access</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

read_write_sub_access

31

32

FUNCTION

33

In this example, we will describe how to read or write sub part of arrays.

34

For example, to write the wavefunction each k point per k point, we need to

35

use the wfs_pw__kpoint_access. This tutorial will show how to use all this

36

kind of <varname>__something_access attributes existing in the different

37

groups (see <a href="../group_level/etsf_io_f90.html#robo123">etsf_main</a> for instance).

38

39

40

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

41

42

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

43

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

44

</pre>

45

46

SOURCE

47

<pre class="source">program read_write_sub_access

48

49

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

50

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

51

52

integer :: i, i_kpt, ncid

53

</pre>

54

NOTES

55

All groups than contain arrays that can have a sub access (on spin or on k points)

56

have attributes built on the following scheme:

57

58

<pre> <short_variable_name>__[spin|kpoint]_access

59

</pre>

60

When all spin or k points values must be read or write at once, one can let

61

the default value (etsf_no_sub_access) ; but if one want to read or write only

62

one spin or one k point, one should put the desired value in this attribute.

63

64

65

All this tutorial is oriented for writing, but it can be adapted easily

66

for reading.

67

68

69

In the beginning of this tutorial, we define an ETSF file with 2 kpoints. This

70

file will contain the kpoints group (<a href="../group_level/etsf_io_f90.html#robo122">etsf_kpoints</a>), the group of wave data

71

(<a href="../group_level/etsf_io_f90.html#robo8">etsf_basisdata</a>) and the main group (<a href="../group_level/etsf_io_f90.html#robo123">etsf_main</a>) with only

72

the coefficient_of_wavefunctions array.

73

74

75

As shown in the first tutorial (<a href="./create_a_crystal_den_file_f90.html#robo5">create_a_crystal_den_file</a>), the classical

76

status variable lstat and error_data are created.

77

78

SOURCE

79

<pre class="source"> logical :: lstat

80

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

81

82

! Specific variables required by the library

83

type(<a href="../group_level/etsf_io_f90.html#robo14">etsf_groups_flags</a>) :: flags

84

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

85

type(<a href="../group_level/etsf_io_f90.html#robo122">etsf_kpoints</a>) :: kpoints

86

type(<a href="../group_level/etsf_io_f90.html#robo8">etsf_basisdata</a>) :: basisdata

87

type(<a href="../group_level/etsf_io_f90.html#robo123">etsf_main</a>) :: main

88

</pre>

89

NOTES

90

The following variables are used in the main program to store the informations.

91

The pointers in the library will be used to point on them. Only some parts of

92

each group will be used.

93

94

<pre> * coef_pw: is a two dimensional array that store all the coefficients of

95

plane waves, but only for one k point.

96

* red_coord_pw_k: is a two dimensional array that stores the coordinates of plane

97

waves for each band, but restricted on one k point.

98

</pre>

99

100

SOURCE

101

<pre class="source"> ! Variables that are declared in the main program in a real case

102

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

103

! Variables that will be used in the basisdata group.

104

integer, allocatable, target :: number_of_coefficients(:)

105

integer, allocatable, target :: red_coord_pw_k(:, :)

106

! Variables that will be used in the kpoints group.

107

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

108

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

109

! Variable to store the definition of the basis set

110

character(len = etsf_charlen), target :: basis

111

</pre>

112

NOTES

113

We set the dimension (2 k points, no spin, 5 bands and 100 planewave

114

coefficients).

115

116

SOURCE

117

<pre class="source"> dims%max_number_of_coefficients = 100

118

dims%max_number_of_states = 5

119

dims%number_of_kpoints = 2

120

dims%number_of_spinor_components = 1

121

dims%number_of_spins = 1

122

dims%real_or_complex_coefficients = 2

123

</pre>

124

NOTES

125

As in the first tutorial (<a href="./create_a_crystal_den_file_f90.html#robo5">create_a_crystal_den_file</a>), we use the high level

126

routine <a href="../group_level/etsf_io_data_init_f90.html#robo26">etsf_io_data_init</a> to define all dimensions and variables for the file

127

we want to create.

128

129

130

In that case, we will use a precise definition of variables, not creating all

131

variables of each included groups. For instance, the basis set will be limited

132

to the required variables for a plane wave description.

133

134

SOURCE

135

<pre class="source"> flags%basisdata = etsf_basisdata_basis_set + &

136

& etsf_basisdata_red_coord_pw + &

137

& etsf_basisdata_n_coeff

138

flags%kpoints = etsf_kpoints_red_coord_kpt + etsf_kpoints_kpoint_weights

139

flags%main = etsf_main_wfs_coeff

140

call <a href="../group_level/etsf_io_data_init_f90.html#robo26">etsf_io_data_init</a>("read_write_sub_access.nc", flags, dims, &

141

& "Tutorial ETSF_IO, use sub access to read or write", &

142

& "Created by the tutorial example of the library", &

143

& lstat, error_data)

144

if (.not. lstat) then

145

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

146

stop

147

end if

148

</pre>

149

NOTES

150

At this time of the example, the disk space to store the wave-function

151

informations has been reserved. In a real case, we let the main program computing

152

the plane waves and the arrays that describe them.

153

154

SOURCE

155

<pre class="source"> write(basis, "(A)") "plane_waves"

156

157

! The main program allocate memory for its computation.

158

allocate(coef_pw_k(2, dims%max_number_of_coefficients * dims%max_number_of_states))

159

allocate(number_of_coefficients(dims%number_of_kpoints))

160

allocate(red_coord_pw_k(3, dims%max_number_of_coefficients))

161

allocate(red_coord_kpt(3, dims%number_of_kpoints))

162

allocate(kpoint_weights(dims%number_of_kpoints))

163

164

! The main program compute all coordinates for k points and plane waves...

165

red_coord_kpt = reshape( (/ 0.0d0, 0.0d0, 0.0d0, &

166

& 0.5d0, 0.5d0, 0.5d0 /), (/ 3, 2 /))

167

kpoint_weights = (/ 0.5d0, 0.5d0 /)

168

number_of_coefficients = (/ dims%max_number_of_coefficients, &

169

& dims%max_number_of_coefficients /)

170

</pre>

171

NOTES

172

To read or write with sub access, there is no high level routine such as

173

<a href="../group_level/etsf_io_data_write_f90.html#robo28">etsf_io_data_write</a>(). Then, we need to open the file and set it a write state.

174

The way to open a file for writing is to use the routine <a href="../low_level/write_routines_f90.html#robo79">etsf_io_low_open_modify</a>()

175

and then to call <a href="../low_level/etsf_io_low_level_f90.html#robo89">etsf_io_low_set_write_mode</a>(). The first call will check that the

176

header is correct.

177

178

179

When the file is not needed anymore, the ncid id must be released and the file

180

closed, using <a href="../low_level/etsf_io_low_level_f90.html#robo64">etsf_io_low_close</a>(). This is mandatory because without this call

181

the write action may be not done.

182

183

SOURCE

184

<pre class="source"> ! Open file for writing

185

call <a href="../low_level/write_routines_f90.html#robo79">etsf_io_low_open_modify</a>(ncid, "read_write_sub_access.nc", &

186

& lstat, error_data = error_data)

187

if (.not. lstat) then

188

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

189

stop

190

end if

191

192

! We switch to write mode.

193

call <a href="../low_level/etsf_io_low_level_f90.html#robo89">etsf_io_low_set_write_mode</a>(ncid, lstat, error_data = error_data)

194

if (.not. lstat) then

195

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

196

stop

197

end if

198

</pre>

199

NOTES

200

We begin the big loop on k points. In this loop, the main program will compute

201

the plane waves and the coordinates of the coefficients. Then, it will use the

202

library to write the values for the current k point.

203

204

SOURCE

205

<pre class="source"> do i_kpt = 1, dims%number_of_kpoints, 1

206

! We compute the plane wave coefficient with the famous

207

! algorithm that works well.

208

do i = 1, dims%max_number_of_coefficients, 1

209

red_coord_pw_k(:, i) = (/ -i, 0, i /)

210

end do

211

coef_pw_k(1, :) = (/ (i, i = 1, &

212

& dims%max_number_of_coefficients * dims%max_number_of_states) /)

213

coef_pw_k(2, :) = (/ (-i, i = 1, &

214

& dims%max_number_of_coefficients * dims%max_number_of_states) /)

215

</pre>

216

NOTES

217

We associate the pointers of groups we want to write with the data in memory.

218

219

SOURCE

220

<pre class="source"> ! We associate the data

221

main%coefficients_of_wavefunctions%data2D => coef_pw_k

222

! We set the sub access.

223

main%wfs_coeff__kpoint_access = i_kpt

224

! Idem for the reduced coordinates of coefficients.

225

basisdata%reduced_coordinates_of_plane_waves%data2D => red_coord_pw_k

226

basisdata%red_coord_pw__kpoint_access = i_kpt

227

</pre>

228

NOTES

229

Now that all the arrays we want to write are associated, we can call the write

230

routine. This routine will read automatically the <var>__kpoint_access attribute

231

and will check the dimensions of the associated arrays.

232

233

SOURCE

234

<pre class="source"> ! We use the group level write routine.

235

call <a href="../group_level/etsf_io_main_put_f90.html#robo103">etsf_io_main_put</a>(ncid, main, lstat, error_data)

236

if (.not. lstat) then

237

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

238

stop

239

end if

240

call <a href="../group_level/etsf_io_basisdata_put_f90.html#robo20">etsf_io_basisdata_put</a>(ncid, basisdata, lstat, error_data)

241

if (.not. lstat) then

242

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

243

stop

244

end if

245

246

! End of the kpoint big loop.

247

end do

248

</pre>

249

NOTES

250

We write the other data that are independent of the kpoint loop.

251

252

WARNINGS

253

It is important to associate to nullify the already used pointers

254

to avoid to write them again.

255

256

SOURCE

257

<pre class="source"> ! We set the associations.

258

kpoints%reduced_coordinates_of_kpoints => red_coord_kpt

259

kpoints%kpoint_weights => kpoint_weights

260

basisdata%basis_set => basis

261

basisdata%reduced_coordinates_of_plane_waves%data2D => null()

262

basisdata%number_of_coefficients => number_of_coefficients

263

! We call the group level write routines.

264

call <a href="../group_level/etsf_io_kpoints_put_f90.html#robo59">etsf_io_kpoints_put</a>(ncid, kpoints, lstat, error_data)

265

if (.not. lstat) then

266

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

267

stop

268

end if

269

call <a href="../group_level/etsf_io_basisdata_put_f90.html#robo20">etsf_io_basisdata_put</a>(ncid, basisdata, lstat, error_data)

270

if (.not. lstat) then

271

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

272

stop

273

end if

274

</pre>

275

NOTES

276

We then set the use_time_reversal_at_gamma attribute for this file using

277

the <a href="../utils/etsf_io_tools_f90.html#robo3">etsf_io_tools</a> module. We write it after the other data since the routine

278

will check that the basis set is indeed a plane wave one and the two variables

279

impacted by this attributes must already exist.

280

281

SOURCE

282

<pre class="source"> call <a href="../utils/etsf_io_tools_f90.html#robo118">etsf_io_tools_set_time_reversal_symmetry</a>(ncid, .false., lstat, error_data)

283

! We handle the error

284

if (.not. lstat) then

285

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

286

stop

287

end if

288

</pre>

289

NOTES

290

As said before, we need to close the file.

291

292

SOURCE

293

<pre class="source"> ! We close the file.

294

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

295

! We handle the error

296

if (.not. lstat) then

297

call <a href="../low_level/etsf_io_low_level_f90.html#robo70">etsf_io_low_error_handle</a>(error_data)

298

stop

299

end if

300

301

! The main program will deallocate its own memory.

302

deallocate(coef_pw_k)

303

deallocate(number_of_coefficients)

304

deallocate(red_coord_pw_k)

305

deallocate(red_coord_kpt)

306

deallocate(kpoint_weights)

307

end program read_write_sub_access

308

</pre>

309

310

</div>

311

312

Generated from ./src/tutorials/read_write_sub_access.f90 with <a href="http://www.xs4all.nl/~rfsber/Robo/robodoc.html">ROBODoc</a> V4.99.30 on Mon Mar 29 2010 11:04:45

313

314

</div>

315

</body>

316

</html>