TABLE OF CONTENTS

ABINIT/m_crystal_io [ Modules ]

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NAME

 m_crystal_io

FUNCTION

 Module containing the methods used to do IO on crystal objects.

COPYRIGHT

  Copyright (C) 2008-2018 ABINIT group (MG, YP, DC)
  This file is distributed under the terms of the
  GNU General Public License, see ~abinit/COPYING
  or http://www.gnu.org/copyleft/gpl.txt .

PARENTS

CHILDREN

SOURCE

21 #if defined HAVE_CONFIG_H
22 #include "config.h"
23 #endif
24 
25 #include "abi_common.h"
26 
27 MODULE m_crystal_io
28 
29  use defs_basis
30  use m_abicore
31  use m_xmpi
32  use m_errors
33  use m_crystal
34  use m_atomdata
35  use m_nctk
36  use iso_c_binding
37 #ifdef HAVE_NETCDF
38  use netcdf
39 #endif
40 
41  use m_fstrings,       only : sjoin, yesno
42  use m_io_tools,       only : file_exists
43  use defs_abitypes,    only : hdr_type
44 
45  implicit none
46 
47  private

m_crystal_io/crystal_from_hdr [ Functions ]

[ Top ] [ m_crystal_io ] [ Functions ]

NAME

  crystal_from_hdr

FUNCTION

  Initializes a crystal_t data type starting from the abinit header.

INPUTS

  hdr<hdr_type>=the abinit header
  timrev ==2 => take advantage of time-reversal symmetry
         ==1 ==> do not use time-reversal symmetry
  remove_inv [optional]= if .TRUE. the inversion symmetry is removed from the set of operations
  even if it is present in the header

OUTPUT

  cryst<crystal_t>= the data type filled with data reported in the abinit header

TODO

  Add information on the use of time-reversal in the Abinit header.

PARENTS

      cut3d,eph,fold2Bloch,gstate,m_ddk,m_dvdb,m_ioarr,m_iowf,m_wfd,m_wfk
      mlwfovlp_qp,mrgscr,setup_bse,setup_screening,setup_sigma,wfk_analyze

CHILDREN

      atomdata_from_znucl,crystal_init

SOURCE

 87 subroutine crystal_from_hdr(cryst,hdr,timrev,remove_inv)
 88 
 89 
 90 !This section has been created automatically by the script Abilint (TD).
 91 !Do not modify the following lines by hand.
 92 #undef ABI_FUNC
 93 #define ABI_FUNC 'crystal_from_hdr'
 94 !End of the abilint section
 95 
 96  implicit none
 97 
 98 !Arguments ------------------------------------
 99  type(hdr_type),intent(in) :: hdr
100  type(crystal_t),intent(out) :: cryst
101  integer,intent(in) :: timrev
102  logical,optional,intent(in) :: remove_inv
103 
104 !Local variables-------------------------------
105  integer :: space_group
106  logical :: rinv,use_antiferro
107 ! *********************************************************************
108 
109  rinv=.FALSE.; if (PRESENT(remove_inv)) rinv=remove_inv
110  use_antiferro = (hdr%nspden==2.and.hdr%nsppol==1)
111 
112  ! Consistency check
113  ABI_CHECK(any(timrev == [1, 2]),"timrev should be in (1|2)")
114  if (use_antiferro) then
115    ABI_CHECK(ANY(hdr%symafm==-1),"Wrong nspden, nsppol, symafm.")
116  end if
117 
118  space_group=0 !FIXME not known
119 
120  call crystal_init(hdr%amu,cryst,space_group,hdr%natom,hdr%npsp,hdr%ntypat,hdr%nsym,hdr%rprimd,hdr%typat,hdr%xred,&
121 & hdr%zionpsp,hdr%znuclpsp,timrev,use_antiferro,rinv,hdr%title,&
122 & symrel=hdr%symrel,tnons=hdr%tnons,symafm=hdr%symafm) ! Optional
123 
124 end subroutine crystal_from_hdr

m_crystal_io/crystal_ncwrite [ Functions ]

[ Top ] [ m_crystal_io ] [ Functions ]

NAME

 crystal_ncwrite

FUNCTION

 Output system geometry to a file, using the NETCDF file format and ETSF I/O.
 Data are taken from the crystal_t object.

INPUTS

  cryst<crystal_t>=Object defining the unit cell and its symmetries.
  ncid=NC file handle.

OUTPUT

  Only writing

NOTES

  Alchemy not treated, since crystal should be initialized at the beginning of the run.

PARENTS

      anaddb,eig2tot,exc_spectra,dfpt_looppert,m_haydock,m_phonons,m_shirley
      outscfcv,sigma

CHILDREN

      atomdata_from_znucl

SOURCE

156 integer function crystal_ncwrite(cryst, ncid) result(ncerr)
157 
158 
159 !This section has been created automatically by the script Abilint (TD).
160 !Do not modify the following lines by hand.
161 #undef ABI_FUNC
162 #define ABI_FUNC 'crystal_ncwrite'
163 !End of the abilint section
164 
165  implicit none
166 
167 !Arguments ------------------------------------
168 !scalars
169  integer,intent(in) :: ncid
170  type(crystal_t),intent(in) :: cryst
171 
172 #ifdef HAVE_NETCDF
173 !Local variables-------------------------------
174 !scalars
175  integer :: itypat
176  character(len=500) :: msg
177  character(len=etsfio_charlen) :: symmorphic
178  type(atomdata_t) :: atom
179 !arrays
180  character(len=2) :: symbols(cryst%ntypat)
181  character(len=80) :: psp_desc(cryst%ntypat),symbols_long(cryst%ntypat)
182 
183 ! *************************************************************************
184 
185  ! @crystal_t
186 
187  ! TODO alchemy not treated correctly
188  if (isalchemical(cryst)) then
189    write(msg,"(3a)")&
190     "Alchemical crystals are not fully supported by the netcdf format",ch10,&
191     "Important parameters (e.g. znucl, symbols) are not written with the correct value"
192    MSG_WARNING(msg)
193  end if
194 
195  symmorphic = yesno(isymmorphic(cryst))
196 
197  ! Define dimensions.
198  ncerr = nctk_def_dims(ncid, [ &
199    nctkdim_t("complex", 2), nctkdim_t("symbol_length", 2),&
200    nctkdim_t("character_string_length", 80), nctkdim_t("number_of_cartesian_directions", 3),&
201    nctkdim_t("number_of_reduced_dimensions", 3), nctkdim_t("number_of_vectors", 3),&
202    nctkdim_t("number_of_atoms", cryst%natom), nctkdim_t("number_of_atom_species", cryst%ntypat),&
203    nctkdim_t("number_of_symmetry_operations", cryst%nsym)], defmode=.True.)
204  NCF_CHECK(ncerr)
205 
206  ! Define variables
207  NCF_CHECK(nctk_def_iscalars(ncid, [character(len=nctk_slen) :: "space_group"]))
208 
209  ncerr = nctk_def_arrays(ncid, [ &
210   ! Atomic structure and symmetry operations
211   nctkarr_t("primitive_vectors", "dp", "number_of_cartesian_directions, number_of_vectors"), &
212   nctkarr_t("reduced_symmetry_matrices", "int", &
213     "number_of_reduced_dimensions, number_of_reduced_dimensions, number_of_symmetry_operations"), &
214   nctkarr_t("reduced_symmetry_translations", "dp", "number_of_reduced_dimensions, number_of_symmetry_operations"), &
215   nctkarr_t("atom_species", "int", "number_of_atoms"), &
216   nctkarr_t("reduced_atom_positions", "dp", "number_of_reduced_dimensions, number_of_atoms"), &
217   nctkarr_t("atomic_numbers", "dp", "number_of_atom_species"), &
218   nctkarr_t("atom_species_names", "char", "character_string_length, number_of_atom_species"), &
219   nctkarr_t("chemical_symbols", "char", "symbol_length, number_of_atom_species"), &
220   nctkarr_t('atomic_mass_units', "dp", "number_of_atom_species"), &
221   ! Atomic information.
222   nctkarr_t("valence_charges", "dp", "number_of_atom_species"), &  ! NB: This variable is not written if alchemical
223   nctkarr_t("pseudopotential_types", "char", "character_string_length, number_of_atom_species") &
224  ])
225  NCF_CHECK(ncerr)
226 
227  ! Some variables require the "symmorphic" attribute.
228  NCF_CHECK(nf90_put_att(ncid, vid("reduced_symmetry_matrices"), "symmorphic", symmorphic))
229  NCF_CHECK(nf90_put_att(ncid, vid("reduced_symmetry_translations"), "symmorphic", symmorphic))
230 
231  ! At this point we have an ETSF-compliant file. Add additional data for internal use in abinit.
232  ! TODO add spinat.
233  ncerr = nctk_def_arrays(ncid, nctkarr_t('symafm', "int", "number_of_symmetry_operations"))
234  NCF_CHECK(ncerr)
235 
236  ! Set-up atomic symbols.
237  do itypat=1,cryst%ntypat
238    call atomdata_from_znucl(atom,cryst%znucl(itypat))
239    symbols(itypat) = atom%symbol
240    write(symbols_long(itypat),'(a2,a78)') symbols(itypat),REPEAT(CHAR(0),78)
241    write(psp_desc(itypat),'(2a)') &
242 &    cryst%title(itypat)(1:MIN(80,LEN_TRIM(cryst%title(itypat)))),REPEAT(CHAR(0),MAX(0,80-LEN_TRIM(cryst%title(itypat))))
243  end do
244 
245  ! Write data.
246  NCF_CHECK(nctk_set_datamode(ncid))
247  NCF_CHECK(nf90_put_var(ncid, vid("space_group"), cryst%space_group))
248  NCF_CHECK(nf90_put_var(ncid, vid("primitive_vectors"), cryst%rprimd))
249  NCF_CHECK(nf90_put_var(ncid, vid("reduced_symmetry_matrices"), cryst%symrel))
250  NCF_CHECK(nf90_put_var(ncid, vid("reduced_symmetry_translations"), cryst%tnons))
251  NCF_CHECK(nf90_put_var(ncid, vid("atom_species"), cryst%typat))
252  NCF_CHECK(nf90_put_var(ncid, vid("reduced_atom_positions"), cryst%xred))
253  NCF_CHECK(nf90_put_var(ncid, vid("atomic_numbers"), cryst%znucl(1:cryst%ntypat)))
254  NCF_CHECK(nf90_put_var(ncid, vid("atom_species_names"), symbols_long))
255  NCF_CHECK(nf90_put_var(ncid, vid("chemical_symbols"), symbols))
256  NCF_CHECK(nf90_put_var(ncid, vid('atomic_mass_units'), cryst%amu))
257  NCF_CHECK(nf90_put_var(ncid, vid("pseudopotential_types"), psp_desc))
258  if (cryst%npsp == cryst%ntypat) then
259    NCF_CHECK(nf90_put_var(ncid, vid("valence_charges"), cryst%zion))
260  end if
261 
262  NCF_CHECK(nf90_put_var(ncid, vid("symafm"), cryst%symafm))
263 
264 #else
265  MSG_ERROR("netcdf library not available")
266 #endif
267 
268 contains
269  integer function vid(vname)
270 
271 
272 !This section has been created automatically by the script Abilint (TD).
273 !Do not modify the following lines by hand.
274 #undef ABI_FUNC
275 #define ABI_FUNC 'vid'
276 !End of the abilint section
277 
278    character(len=*),intent(in) :: vname
279    vid = nctk_idname(ncid, vname)
280  end function vid
281 
282 end function crystal_ncwrite

m_crystal_io/crystal_ncwrite_path [ Functions ]

[ Top ] [ m_crystal_io ] [ Functions ]

NAME

 crystal_ncwrite_path

FUNCTION

 Output system geometry to a file, using the NETCDF file format and ETSF I/O.

INPUTS

  crystal<crystal_t>=Object defining the unit cell and its symmetries.
  path=filename

OUTPUT

  Only writing

PARENTS

CHILDREN

SOURCE

307 integer function crystal_ncwrite_path(crystal, path) result(ncerr)
308 
309 
310 !This section has been created automatically by the script Abilint (TD).
311 !Do not modify the following lines by hand.
312 #undef ABI_FUNC
313 #define ABI_FUNC 'crystal_ncwrite_path'
314 !End of the abilint section
315 
316  implicit none
317 
318 !Arguments ------------------------------------
319 !scalars
320  character(len=*),intent(in) :: path
321  type(crystal_t),intent(in) :: crystal
322 
323 #ifdef HAVE_NETCDF
324 !Local variables-------------------------------
325 !scalars
326  integer :: ncid
327 
328 ! *************************************************************************
329 
330  ncerr = nf90_noerr
331  if (file_exists(path)) then
332    NCF_CHECK(nctk_open_modify(ncid, path, xmpi_comm_self))
333  else
334    ncerr = nctk_open_create(ncid, path, xmpi_comm_self)
335    NCF_CHECK_MSG(ncerr, sjoin("creating:", path))
336  end if
337 
338  NCF_CHECK(crystal_ncwrite(crystal, ncid))
339  NCF_CHECK(nf90_close(ncid))
340 #endif
341 
342 end function crystal_ncwrite_path