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1 : : !!****m* ABINIT/m_lwf_ncfile
2 : : !! NAME
3 : : !! m_lwf_ncfile
4 : : !!
5 : : !! FUNCTION
6 : : !! This module contains the subroutines for output netcdf file
7 : : !!
8 : : !!
9 : : !! Datatypes:
10 : : !! lwf_ncfile_t: store data to calculate lwf_ncfile
11 : : !!
12 : : !!
13 : : !! COPYRIGHT
14 : : !! Copyright (C) 2001-2026 ABINIT group (hexu)
15 : : !! This file is distributed under the terms of the
16 : : !! GNU General Public License, see ~abinit/COPYING
17 : : !! or http://www.gnu.org/copyleft/gpl.txt .
18 : : !! For the initials of contributors, see ~abinit/doc/developers/contributors.txt .
19 : : !!
20 : : !! SOURCE
21 : :
22 : :
23 : : #if defined HAVE_CONFIG_H
24 : : #include "config.h"
25 : : #endif
26 : :
27 : : #include "abi_common.h"
28 : :
29 : : module m_lwf_ncfile
30 : :
31 : : use defs_basis
32 : : use m_abicore
33 : : use m_errors
34 : : use m_xmpi
35 : : use m_nctk
36 : : use m_lwf_hist , only: lwf_hist_t
37 : : use m_lwf_primitive_potential, only: lwf_primitive_potential_t
38 : : use m_lwf_potential , only: lwf_potential_t
39 : : use m_multibinit_dataset, only: multibinit_dtset_type
40 : : use m_multibinit_cell, only: mbcell_t, mbsupercell_t
41 : : use m_lwf_observables, only : lwf_observables_t
42 : : #if defined HAVE_NETCDF
43 : : use netcdf
44 : : #endif
45 : : implicit none
46 : :
47 : : private
48 : : !!***
49 : : type, public :: lwf_ncfile_t
50 : : logical :: isopen=.False. ! if the file is open
51 : : ! dimensions
52 : : integer :: three, nlwf
53 : : ! three: 3
54 : :
55 : : ! file id
56 : : integer :: ncerr, ncid
57 : : ! variable id
58 : : integer :: lwf_id, time_id, itime_id, etotal_id, entropy_id, displacement_id
59 : : integer :: ilwf_prim_id, rvec_id, lwf_masses_id, natom_id
60 : : integer :: itime, ntime,ncell
61 : : ! itime: time index
62 : : integer :: write_traj=1
63 : : !whether to write the trajectory
64 : : character(len=fnlen) :: filename
65 : :
66 : : ! netcdf filename
67 : : logical :: has_constrain=.False.
68 : : integer :: n_fixed_lwf
69 : : integer, allocatable :: fixed_lwf_ids(:)
70 : : real(dp), allocatable :: fixed_lwf_values(:)
71 : : contains
72 : : ! initialize
73 : : procedure :: initialize
74 : : procedure :: finalize
75 : : procedure :: def_lwf_var
76 : : procedure :: write_cell
77 : : procedure :: write_one_step
78 : : end type lwf_ncfile_t
79 : :
80 : : contains
81 : 7 : subroutine initialize(self, filename, write_traj)
82 : : class(lwf_ncfile_t) :: self
83 : : character(len=*),intent(in) :: filename
84 : : integer, intent(in) :: write_traj
85 : : integer :: ncerr
86 : 7 : self%itime=0
87 : 7 : self%write_traj=write_traj
88 : 7 : self%filename=trim(filename)
89 : : #if defined HAVE_NETCDF
90 : 7 : write(std_out,*) "Write iteration in lwf history file "//trim(self%filename)//"."
91 : : ! Create netCDF file
92 : 7 : ncerr = nf90_create(path=trim(self%filename), cmode=NF90_NETCDF4, ncid=self%ncid)
93 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when creating netcdf history file")
94 : 7 : self%isopen=.True.
95 : 7 : ncerr =nf90_enddef(self%ncid)
96 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when ending def mode in lwf netcdf history file")
97 : : #endif
98 [ + - ]: 7 : end subroutine initialize
99 : :
100 : 7 : subroutine finalize(self)
101 : : class(lwf_ncfile_t), intent(inout) :: self
102 : : #if defined HAVE_NETCDF
103 : : integer :: ncerr
104 [ + - ]: 7 : if (self%isopen) then
105 : 7 : write(std_out, *) "Closing lwf history file "//trim(self%filename)//"."
106 : 7 : ncerr=nf90_close(self%ncid)
107 [ - + - - ]: 7 : NCF_CHECK_MSG(ncerr, "close netcdf lwf history file"//trim(self%filename)//".")
108 : : end if
109 : : #endif
110 : 7 : end subroutine finalize
111 : :
112 : 7 : subroutine write_cell(self, supercell)
113 : : class(lwf_ncfile_t), intent(inout) :: self
114 : : type(mbsupercell_t), intent(in) :: supercell
115 : : integer :: ncerr, natom3, nnz, id_nnz, id_natom3, id_map_ilwf, id_map_idisp, id_map_val
116 : : integer :: latt_rvec_id, ilatt_prim_id, ref_cell_id, ref_xcart_id, zion_id, masses_id
117 : : #if defined HAVE_NETCDF
118 : 7 : ncerr = nf90_redef(self%ncid)
119 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when starting defining trajectory variables in lwf history file.")
120 : : ! define dimensions
121 : 7 : ncerr=nf90_def_dim(self%ncid, "three", 3, self%three)
122 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining dimension three in history file.")
123 : :
124 : 7 : ncerr=nf90_def_dim(self%ncid, "nlwf", supercell%lwf%nlwf, self%nlwf)
125 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining dimension nlwf in history file.")
126 : :
127 : :
128 : 7 : ncerr=nf90_def_dim(self%ncid, "natom", supercell%lattice%natom, self%natom_id)
129 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining dimension natom in history file.")
130 : :
131 : :
132 : 7 : natom3=supercell%lwf%lwf_latt_coeffs%coeffs%mshape(1)
133 : 7 : ncerr=nf90_def_dim(self%ncid, "natom3", natom3, id_natom3)
134 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining dimension natom3 in history file.")
135 : :
136 : 7 : nnz=supercell%lwf%lwf_latt_coeffs%coeffs%nnz
137 : 7 : ncerr=nf90_def_dim(self%ncid, "lwf_latt_map_nnz",nnz, id_nnz)
138 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining dimension nlwf in history file.")
139 : :
140 : : !ncerr=nf90_def_dim(self%ncid, "nR", 3, self%nlwf)
141 : : !NCF_CHECK_MSG(ncerr, "Error when defining dimension three in history file.")
142 : :
143 : : call ab_define_var(self%ncid, [self%three, self%nlwf], &
144 [ + + ]: 21 : & self%rvec_id, NF90_INT, "lwf_rvec", "R-vectors for LWF ", "dimensionless")
145 : :
146 : : call ab_define_var(self%ncid, [self%nlwf], &
147 : : & self%ilwf_prim_id, NF90_INT, "ilwf_prim", &
148 [ + + ]: 14 : & "index of lwf in primitive cell", "dimensionless")
149 : :
150 : : call ab_define_var(self%ncid, [self%nlwf], &
151 [ + + ]: 14 : & self%lwf_masses_id, NF90_DOUBLE, "lwf_masses", "LWF MASSES", "dimensionless")
152 : :
153 : :
154 : : ! Lattice
155 : : call ab_define_var(self%ncid, [self%three, self%natom_id], &
156 [ + + ]: 21 : & latt_rvec_id, NF90_INT, "lattice_rvec", "R-vectors for LATTICE ", "dimensionless")
157 : :
158 : : call ab_define_var(self%ncid, [self%natom_id], &
159 : : & ilatt_prim_id, NF90_INT, "ilatt_prim", &
160 [ + + ]: 14 : & "index of lattice in primitive cell", "dimensionless")
161 : :
162 : :
163 : : call ab_define_var(self%ncid, [self%three,self%three], &
164 : : & ref_cell_id, NF90_DOUBLE, "ref_cell", &
165 [ + + ]: 21 : & "REFerence CELL", "bohr")
166 : :
167 : : call ab_define_var(self%ncid, [self%three,self%natom_id], &
168 : : & ref_xcart_id, NF90_DOUBLE, "ref_xcart", &
169 [ + + ]: 21 : & "REFerence XCART", "bohr")
170 : :
171 : : call ab_define_var(self%ncid, [self%natom_id], &
172 : : & zion_id, NF90_INT, "zion", &
173 [ + + ]: 14 : & "ZION", "dimensionless")
174 : :
175 : : call ab_define_var(self%ncid, [self%natom_id], &
176 : : & masses_id, NF90_DOUBLE, "masses", &
177 [ + + ]: 14 : & "MASSES", "dimensionless")
178 : :
179 : :
180 : :
181 : : ! define vars for lwf lattice displacement mapping in the format of a COO matrix.
182 : : call ab_define_var(self%ncid, [id_nnz], id_map_idisp, &
183 : : & NF90_INT, "lwf_latt_map_id_displacement", &
184 [ + + ]: 14 : & "LWF lattice mapping coefficient COO matrix displacement id", "dimensionless")
185 : :
186 : 7 : ncerr=nf90_def_var_deflate(self%ncid, id_map_idisp, shuffle=1, deflate=1, deflate_level=2)
187 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining deflating for variable id_map_idisp")
188 : :
189 : :
190 : :
191 : : call ab_define_var(self%ncid, [id_nnz], id_map_ilwf,&
192 : : & NF90_INT, "lwf_latt_map_id_lwf", &
193 [ + + ]: 14 : & "LWF lattice mapping coefficient COO matrix LWF id","dimensionless")
194 : :
195 : 7 : ncerr=nf90_def_var_deflate(self%ncid, id_map_ilwf, shuffle=1, deflate=1, deflate_level=2)
196 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining delfating for variable id_map_ilwf")
197 : :
198 : :
199 : : call ab_define_var(self%ncid, [id_nnz], id_map_val, &
200 : : & NF90_DOUBLE, "lwf_latt_map_values", &
201 [ + + ]: 14 : & "LWF lattice mapping coefficient COO matrix values","dimensionless")
202 : :
203 : 7 : ncerr=nf90_def_var_deflate(self%ncid, id_map_val, shuffle=1, deflate=1, deflate_level=2)
204 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining delfating for variable id_map_val")
205 : :
206 : 7 : ncerr=nf90_enddef(self%ncid)
207 : :
208 : :
209 : :
210 : : ncerr=nf90_put_var(self%ncid, zion_id, [supercell%lattice%zion], &
211 [ + - + + : 43029 : & start=[1], count=[supercell%lattice%natom])
+ - + + +
+ ]
212 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting zion in lattice history file.")
213 : :
214 : : ncerr=nf90_put_var(self%ncid, masses_id, [supercell%lattice%masses], &
215 [ + - + + : 43029 : & start=[1], count=[supercell%lattice%natom])
+ - + + +
+ ]
216 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting masses in lattice history file.")
217 : :
218 : : ncerr=nf90_put_var(self%ncid, ref_xcart_id, [supercell%lattice%xcart], &
219 [ + - + + : 150556 : & start=[1,1], count=[3,supercell%lattice%natom])
+ + + - +
+ + + ]
220 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting ref_xcart in lattice history file.")
221 : :
222 : : ncerr=nf90_put_var(self%ncid, ref_cell_id, [supercell%lattice%cell], &
223 [ + + + + : 154 : & start=[1,1], count=[3,3])
+ + ]
224 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting ref_cell in lattice history file.")
225 : :
226 : :
227 : :
228 : : ncerr=nf90_put_var(self%ncid, self%ilwf_prim_id, [supercell%lwf%ilwf_prim], &
229 [ + - + + : 14357 : & start=[1], count=[supercell%lwf%nlwf])
+ - + + +
+ ]
230 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting ilwf_prim in lwf history file.")
231 : :
232 : : ncerr=nf90_put_var(self%ncid, self%rvec_id, [supercell%lwf%rvec], &
233 [ + - + + : 50204 : & start=[1,1], count=[3, supercell%lwf%nlwf])
+ + + - +
+ + + ]
234 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting lwf rvec in lwf history file.")
235 : :
236 : : ncerr=nf90_put_var(self%ncid, self%lwf_masses_id, [supercell%lwf%lwf_masses], &
237 [ + - + + : 14357 : & start=[1], count=[supercell%lwf%nlwf])
+ - + + +
+ ]
238 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting lwf_masses in lwf history file.")
239 : :
240 : : ncerr=nf90_put_var(self%ncid, id_map_idisp, &
241 : : & supercell%lwf%lwf_latt_coeffs%coeffs%ind%data(1, 1:nnz), &
242 [ + + ]: 14 : & start=[1], count=[nnz])
243 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting id_map_idisp in lwf history file.")
244 : :
245 : :
246 : : ncerr=nf90_put_var(self%ncid, id_map_ilwf, &
247 : : & supercell%lwf%lwf_latt_coeffs%coeffs%ind%data(2, 1:nnz), &
248 [ + + ]: 14 : & start=[1], count=[nnz])
249 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting id_map_ilwf in lwf history file.")
250 : :
251 : :
252 : : ncerr=nf90_put_var(self%ncid, id_map_val, &
253 : : & supercell%lwf%lwf_latt_coeffs%coeffs%val%data(1:nnz), &
254 [ + + ]: 14 : & start=[1], count=[nnz])
255 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when writting id_map_ilwf in lwf history file.")
256 : :
257 : :
258 : : #endif
259 : :
260 : 7 : end subroutine write_cell
261 : :
262 : 7 : subroutine def_lwf_var(self, hist)
263 : : class(lwf_ncfile_t), intent(inout) :: self
264 : : type(lwf_hist_t),intent(in) :: hist
265 : : integer :: ncerr
266 : 7 : ABI_UNUSED_A(hist)
267 : :
268 : : #if defined HAVE_NETCDF
269 : 7 : ncerr = nf90_redef(self%ncid)
270 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when starting defining trajectory variables in lwf history file.")
271 : : ! define dimensions
272 : 7 : ncerr=nf90_def_dim(self%ncid, "ntime", nf90_unlimited, self%ntime)
273 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining dimension ntime in lwf history file.")
274 : : !call ab_define_var(ncid,dim1,typat_id,NF90_DOUBLE,&
275 : : ! & "typat","types of atoms","dimensionless" )
276 : :
277 : : !if(self%write_traj==1) then
278 : : call ab_define_var(self%ncid, (/ self%nlwf, self%ntime /), &
279 [ + + ]: 21 : & self%lwf_id, NF90_DOUBLE, "lwf", "lwf amplitude", "dimensionless")
280 : :
281 : 7 : ncerr=nf90_def_var_deflate(self%ncid, self%lwf_id, shuffle=1, deflate=1, deflate_level=2)
282 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when defining deflating for variable lwf")
283 : :
284 : : !endif
285 : :
286 : : !call ab_define_var(self%ncid, (/ self%ntime /), &
287 : : ! & self%time_id, NF90_DOUBLE, "time", "time", "s")
288 : : call ab_define_var(self%ncid, (/ self%ntime /), &
289 [ + + ]: 14 : & self%etotal_id, NF90_DOUBLE, "etotal", "TOTAL energy", "Ha")
290 : : !call ab_define_var(self%ncid, (/ self%ntime /), &
291 : : ! & self%entropy_id, NF90_DOUBLE, "entropy", "Entropy", "Joule/K")
292 : :
293 : : call ab_define_var(self%ncid, (/ self%ntime /), &
294 [ + + ]: 14 : & self%itime_id, NF90_INT, "itime", "index of time in timeline", "1")
295 : :
296 : 7 : ncerr=nf90_enddef(self%ncid)
297 [ - + ]: 7 : NCF_CHECK_MSG(ncerr, "Error when finishing defining variables in lwf history file.")
298 : : #endif
299 : :
300 : 7 : end subroutine def_lwf_var
301 : :
302 : :
303 : :
304 : 217 : subroutine write_one_step(self, hist)
305 : : class(lwf_ncfile_t), intent(inout) :: self
306 : : type(lwf_hist_t), intent(in) :: hist
307 : : integer :: ncerr, itime
308 : 217 : self%itime=self%itime+1
309 : 217 : itime = self%itime
310 : :
311 : : #if defined HAVE_NETCDF
312 : : !if(self%write_traj ==1) then
313 : : !print *, "Write one step of netcdf."
314 : : ncerr=nf90_put_var(self%ncid, self%lwf_id, hist%current_lwf, &
315 [ + + + + ]: 1085 : & start=[1, itime], count=[hist%nlwf, 1])
316 [ - + ]: 217 : NCF_CHECK_MSG(ncerr, "Error when writting lwf amplitudes in lwf history file.")
317 : : !end if
318 : :
319 : : ncerr=nf90_put_var(self%ncid, self%etotal_id, [hist%current_energy], &
320 [ + + + + ]: 651 : & start=[itime], count=[1])
321 [ - + ]: 217 : NCF_CHECK_MSG(ncerr, "Error when writting energy in lwf history file.")
322 : :
323 : : ncerr=nf90_put_var(self%ncid, self%itime_id, [self%itime], &
324 [ + + + + ]: 651 : & start=[itime], count=[1])
325 [ - + ]: 217 : NCF_CHECK_MSG(ncerr, "Error when writting energy in lwf history file.")
326 : :
327 : : !ncerr=nf90_put_var(self%ncid, self%displacement_id, [displacement], &
328 : : ! & start=[1,itime], count=[3, hist%natom, 1])
329 : : !NCF_CHECK_MSG(ncerr, "Error when writting energy in lwf history file.")
330 : :
331 : : #endif
332 : :
333 : 217 : end subroutine write_one_step
334 : :
335 : :
336 [ # # # # : 0 : end module m_lwf_ncfile
# # # # #
# # # #
# ]
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