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1 : : !!****m* ABINIT/m_lattice_ncfile
2 : : !! NAME
3 : : !! m_lattice_ncfile
4 : : !!
5 : : !! FUNCTION
6 : : !! This module contains the subroutines for output netcdf file
7 : : !!
8 : : !! Datatypes:
9 : : !! lattice_ncfile_t: store data to calculate lattice_ncfile
10 : : !!
11 : : !! COPYRIGHT
12 : : !! Copyright (C) 2001-2026 ABINIT group (hexu)
13 : : !! This file is distributed under the terms of the
14 : : !! GNU General Public License, see ~abinit/COPYING
15 : : !! or http://www.gnu.org/copyleft/gpl.txt .
16 : : !! For the initials of contributors, see ~abinit/doc/developers/contributors.txt .
17 : : !!
18 : : !! SOURCE
19 : :
20 : :
21 : : #if defined HAVE_CONFIG_H
22 : : #include "config.h"
23 : : #endif
24 : :
25 : : #include "abi_common.h"
26 : :
27 : :
28 : : module m_lattice_ncfile
29 : :
30 : : use defs_basis
31 : : use m_abicore
32 : : use m_errors
33 : : use m_xmpi
34 : : use m_nctk
35 : : use m_lattice_harmonic_primitive_potential, only: lattice_harmonic_primitive_potential_t
36 : : use m_lattice_harmonic_potential , only: lattice_harmonic_potential_t
37 : : use m_multibinit_dataset, only: multibinit_dtset_type
38 : : use m_multibinit_cell, only: mbcell_t, mbsupercell_t
39 : : use netcdf
40 : :
41 : : implicit none
42 : :
43 : : private
44 : : !!***
45 : : type, public :: lattice_ncfile_t
46 : : logical :: isopen=.False. ! if the file is open
47 : : ! dimensions
48 : : integer :: three, natom
49 : : ! three: 3
50 : :
51 : : ! file id
52 : : integer :: ncerr, ncid
53 : : ! variable id
54 : : integer :: vcart_id, xcart_id, cell_id, time_id, itime_id, etotal_id, ekin_id, entropy_id
55 : : integer :: ilatt_prim_id, rvec_id, zion_id, masses_id, ref_xcart_id, ref_cell_id
56 : : integer :: itime, ntime,ncell
57 : : ! itime: time index
58 : : integer :: write_traj=1
59 : : !whether to write the trajectory
60 : : character(len=fnlen) :: filename
61 : : ! netcdf filename
62 : : contains
63 : : ! initialize
64 : : procedure :: initialize
65 : : procedure :: finalize
66 : : procedure :: def_lattice_var
67 : : procedure :: write_cell
68 : : procedure :: write_one_step
69 : : end type lattice_ncfile_t
70 : :
71 : : contains
72 : 3 : subroutine initialize(self, filename, write_traj)
73 : : class(lattice_ncfile_t) :: self
74 : : character(len=*),intent(in) :: filename
75 : : integer, intent(in) :: write_traj
76 : : integer :: ncerr
77 : 3 : self%itime=0
78 : 3 : self%write_traj=write_traj
79 : 3 : self%filename=trim(filename)
80 : 3 : write(std_out,*) "Write iteration in lattice history file "//trim(self%filename)//"."
81 : : ! Create netCDF file
82 : 3 : ncerr = nf90_create(path=trim(filename), cmode=NF90_CLOBBER, ncid=self%ncid)
83 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when creating netcdf history file")
84 : 3 : self%isopen=.True.
85 : 3 : ncerr =nf90_enddef(self%ncid)
86 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when ending def mode in lattice netcdf history file")
87 [ + - ]: 3 : end subroutine initialize
88 : :
89 : 3 : subroutine finalize(self)
90 : : class(lattice_ncfile_t), intent(inout) :: self
91 : : integer :: ncerr
92 [ + - ]: 3 : if (self%isopen) then
93 : 3 : write(std_out, *) "Closing lattice history file "//trim(self%filename)//"."
94 : 3 : ncerr=nf90_close(self%ncid)
95 [ - + - - ]: 3 : NCF_CHECK_MSG(ncerr, "close netcdf lattice history file"//trim(self%filename)//".")
96 : : end if
97 : :
98 : 3 : end subroutine finalize
99 : :
100 : 3 : subroutine write_cell(self, supercell)
101 : : class(lattice_ncfile_t), intent(inout) :: self
102 : : type(mbsupercell_t), intent(in) :: supercell
103 : : integer :: ncerr
104 : :
105 : 3 : ncerr = nf90_redef(self%ncid)
106 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when starting defining trajectory variables in lattice history file.")
107 : : ! define dimensions
108 : 3 : ncerr=nf90_def_dim(self%ncid, "three", 3, self%three)
109 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when defining dimension three in history file.")
110 : :
111 : 3 : ncerr=nf90_def_dim(self%ncid, "natom", supercell%lattice%natom, self%natom)
112 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when defining dimension natom in history file.")
113 : :
114 : : call ab_define_var(self%ncid, [self%three, self%natom], &
115 [ + + ]: 9 : & self%rvec_id, NF90_INT, "lattice_rvec", "R-vectors for LATTICE ", "dimensionless")
116 : :
117 : : call ab_define_var(self%ncid, [self%natom], &
118 : : & self%ilatt_prim_id, NF90_INT, "ilatt_prim", &
119 [ + + ]: 6 : & "index of lattice in primitive cell", "dimensionless")
120 : :
121 : :
122 : : call ab_define_var(self%ncid, [self%three,self%three], &
123 : : & self%ref_cell_id, NF90_DOUBLE, "ref_cell", &
124 [ + + ]: 9 : & "REFerence CELL", "bohr")
125 : :
126 : :
127 : :
128 : : call ab_define_var(self%ncid, [self%three,self%natom], &
129 : : & self%ref_xcart_id, NF90_DOUBLE, "ref_xcart", &
130 [ + + ]: 9 : & "REFerence XCART", "bohr")
131 : :
132 : : call ab_define_var(self%ncid, [self%natom], &
133 : : & self%zion_id, NF90_INT, "zion", &
134 [ + + ]: 6 : & "ZION", "dimensionless")
135 : :
136 : : call ab_define_var(self%ncid, [self%natom], &
137 : : & self%masses_id, NF90_DOUBLE, "masses", &
138 [ + + ]: 6 : & "MASSES", "dimensionless")
139 : :
140 : :
141 : 3 : Ncerr=nf90_enddef(self%ncid)
142 : :
143 : : ! ncerr=nf90_put_var(self%ncid, self%ilatt_prim_id, [supercell%lattice%ilatt_prim], &
144 : : ! & start=[1], count=[supercell%lattice%natom])
145 : : ! NCF_CHECK_MSG(ncerr, "Error when writting ilatt_prim in lattice history file.")
146 : :
147 : : ! ncerr=nf90_put_var(self%ncid, self%rvec_id, [supercell%lattice%rvec], &
148 : : ! & start=[1,1], count=[3, supercell%lattice%natom])
149 : : ! NCF_CHECK_MSG(ncerr, "Error when writting ilatt_prim in lattice history file.")
150 : :
151 : : ncerr=nf90_put_var(self%ncid, self%zion_id, [supercell%lattice%zion], &
152 [ + - + + : 4969 : & start=[1], count=[supercell%lattice%natom])
+ - + + +
+ ]
153 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when writting zion in lattice history file.")
154 : :
155 : : ncerr=nf90_put_var(self%ncid, self%masses_id, [supercell%lattice%masses], &
156 [ + - + + : 4969 : & start=[1], count=[supercell%lattice%natom])
+ - + + +
+ ]
157 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when writting masses in lattice history file.")
158 : :
159 : : ncerr=nf90_put_var(self%ncid, self%ref_xcart_id, [supercell%lattice%xcart], &
160 [ + - + + : 17372 : & start=[1,1], count=[3,supercell%lattice%natom])
+ + + - +
+ + + ]
161 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when writting ref_xcart in lattice history file.")
162 : :
163 : : ncerr=nf90_put_var(self%ncid, self%ref_cell_id, [supercell%lattice%cell], &
164 [ + + + + : 66 : & start=[1,1], count=[3,3])
+ + ]
165 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when writting ref_cell in lattice history file.")
166 : :
167 : 3 : end subroutine write_cell
168 : :
169 : 3 : subroutine def_lattice_var(self)
170 : : class(lattice_ncfile_t), intent(inout) :: self
171 : : !type(lattice_hist_t),intent(in) :: hist
172 : : integer :: ncerr
173 : :
174 : 3 : ncerr = nf90_redef(self%ncid)
175 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when starting defining trajectory variables in lattice history file.")
176 : : ! define dimensions
177 : 3 : ncerr=nf90_def_dim(self%ncid, "ntime", nf90_unlimited, self%ntime)
178 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when defining dimension ntime in lattice history file.")
179 : : !call ab_define_var(ncid,dim1,typat_id,NF90_DOUBLE,&
180 : : ! & "typat","types of atoms","dimensionless" )
181 : :
182 : : !if(self%write_traj==1) then
183 : : call ab_define_var(self%ncid, (/self%three, self%natom, self%ntime /), &
184 [ + + ]: 12 : & self%xcart_id, NF90_DOUBLE, "xcart", "lattice amplitude", "bohr")
185 : : call ab_define_var(self%ncid, (/self%three, self%natom, self%ntime /), &
186 [ + + ]: 12 : & self%vcart_id, NF90_DOUBLE, "vcart", "cartesian velocity", "bohr/a.u.")
187 : : call ab_define_var(self%ncid, (/self%three, self%three, self%ntime /), &
188 [ + + ]: 12 : & self%cell_id, NF90_DOUBLE, "cell", "cell parameters", "bohr")
189 : :
190 : :
191 : : !endif
192 : :
193 : : !call ab_define_var(self%ncid, (/ self%ntime /), &
194 : : ! & self%time_id, NF90_DOUBLE, "time", "time", "s")
195 : : call ab_define_var(self%ncid, (/ self%ntime /), &
196 [ + + ]: 6 : & self%etotal_id, NF90_DOUBLE, "etotal", "TOTAL energy", "Ha")
197 : : call ab_define_var(self%ncid, (/ self%ntime /), &
198 [ + + ]: 6 : & self%ekin_id, NF90_DOUBLE, "ekin", "Kinetic energy", "Ha")
199 : :
200 : : !call ab_define_var(self%ncid, (/ self%ntime /), &
201 : : ! & self%entropy_id, NF90_DOUBLE, "entropy", "Entropy", "Joule/K")
202 : :
203 : : call ab_define_var(self%ncid, (/ self%ntime /), &
204 [ + + ]: 6 : & self%itime_id, NF90_INT, "itime", "index of time in timeline", "1")
205 : :
206 : 3 : ncerr=nf90_enddef(self%ncid)
207 [ - + ]: 3 : NCF_CHECK_MSG(ncerr, "Error when finishing defining variables in lattice history file.")
208 : :
209 : 3 : end subroutine def_lattice_var
210 : :
211 : :
212 : :
213 [ - + - + ]: 213 : subroutine write_one_step(self, xcart, vcart, Etotal, Ek)
214 : : class(lattice_ncfile_t), intent(inout) :: self
215 : : !type(lattice_hist_t), intent(in) :: hist
216 : : real(dp) , intent(in) :: Etotal, Ek, xcart(:,:), vcart(:,:)
217 : : integer :: ncerr, itime, natom
218 : 213 : natom=size(xcart, 2)
219 : 213 : self%itime=self%itime+1
220 : 213 : itime = self%itime
221 : :
222 : : !if(self%write_traj ==1) then
223 : : ncerr=nf90_put_var(self%ncid, self%xcart_id, xcart, &
224 [ + + + + ]: 1491 : & start=[1,1, itime], count=[3,natom, 1])
225 : :
226 : : ncerr=nf90_put_var(self%ncid, self%vcart_id, vcart, &
227 [ + + + + ]: 1491 : & start=[1,1, itime], count=[3,natom, 1])
228 : :
229 [ - + ]: 213 : NCF_CHECK_MSG(ncerr, "Error when writting lattice amplitudes in lattice history file.")
230 : : !end if
231 : :
232 : : ncerr=nf90_put_var(self%ncid, self%etotal_id, [Etotal], &
233 [ + + + + ]: 639 : & start=[itime], count=[1])
234 [ - + ]: 213 : NCF_CHECK_MSG(ncerr, "Error when writting total energy in lattice history file.")
235 : :
236 : : ncerr=nf90_put_var(self%ncid, self%ekin_id, [Ek], &
237 [ + + + + ]: 639 : & start=[itime], count=[1])
238 [ - + ]: 213 : NCF_CHECK_MSG(ncerr, "Error when writting kinetic energy in lattice history file.")
239 : :
240 : : ncerr=nf90_put_var(self%ncid, self%itime_id, [self%itime], &
241 [ + + + + ]: 639 : & start=[itime], count=[1])
242 [ - + ]: 213 : NCF_CHECK_MSG(ncerr, "Error when writting itime in lattice history file.")
243 : :
244 : 213 : end subroutine write_one_step
245 : :
246 : : subroutine close(self)
247 : : class(lattice_ncfile_t) :: self
248 : : self%isopen=.False.
249 : : end subroutine close
250 : :
251 : :
252 : 0 : end module m_lattice_ncfile
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