TABLE OF CONTENTS

ABINIT/m_fit_data [ Modules ]

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NAME

 m_fit_data

FUNCTION

COPYRIGHT

 Copyright (C) 2010-2024 ABINIT group (AM)
 This file is distributed under the terms of the
 GNU General Public Licence, see ~abinit/COPYING
 or http://www.gnu.org/copyleft/gpl.txt .
 For the initials of contributors, see ~abinit/doc/developers/contributors.txt .

SOURCE

18 #if defined HAVE_CONFIG_H
19 #include "config.h"
20 #endif
21 
22 #include "abi_common.h"
23 
24 module m_fit_data
25 
26  use defs_basis
27  use m_errors
28  use m_abicore
29 
30  use m_geometry,     only : metric
31  
32  implicit none

m_fit_data/fit_data_compute [ Functions ]

[ Top ] [ m_fit_data ] [ Functions ]

NAME

 fit_data_compute

FUNCTION

 Conpute the strain of each configuration.
 Compute the displacmeent of each configuration.
 Compute the variation of the displacement due to strain of each configuration.
 Compute fixed forces and stresse and get the standard deviation.
 Compute Sheppard and al Factors  \Omega^{2} see J.Chem Phys 136, 074103 (2012) [[cite:Sheppard2012]]

INPUTS

 eff_pot<type(effective_potential)> = effective potential
 hist<type(abihist)> = The history of the MD (or snapshot of DFT
 comm = MPI communicator
 verbose  = optional, flag for the verbose mode

OUTPUT

 fit_data<fit_data_type> = fit_data is now filled

SOURCE

279 subroutine fit_data_compute(fit_data,eff_pot,hist,comm,verbose)
280 
281  use m_strain,only : strain_type,strain_get
282  use m_effective_potential,only : effective_potential_type,effective_potential_evaluate
283  use m_effective_potential,only : effective_potential_getDisp
284  use m_abihist, only : abihist
285  use m_strain,only : strain_type,strain_get
286  implicit none
287   
288 !Arguments ------------------------------------
289 !scalars
290  integer,intent(in) :: comm
291  logical,optional,intent(in) :: verbose
292  !arrays
293  type(fit_data_type),intent(inout) :: fit_data
294  type(effective_potential_type),intent(in) :: eff_pot
295  type(abihist),intent(in) :: hist
296 !Local variables-------------------------------
297 !scalar
298  integer :: ii,itime,natom,ntime
299  real(dp):: energy
300  logical :: need_verbose
301 !arrays
302  character(len=500) :: message
303  real(dp) :: gmet(3,3),gprimd(3,3),rmet(3,3)
304  real(dp),allocatable :: energy_diff(:)
305  real(dp),allocatable :: du_delta(:,:,:,:),displacement(:,:,:),strain(:,:)
306  real(dp),allocatable :: fcart_diff(:,:,:),gred_fixed(:,:,:),fcart_fixed(:,:,:)
307  real(dp),allocatable :: strten_diff(:,:),strten_fixed(:,:),sqomega(:),ucvol(:)
308  type(strain_type) :: strain_t
309  type(training_set_type) :: ts
310 ! *************************************************************************
311 
312 !Initialisation of optional arguments
313  need_verbose = .TRUE.
314  if(present(verbose)) need_verbose = verbose
315 
316 !Checks
317  natom = eff_pot%supercell%natom
318  ntime = hist%mxhist
319  if(natom /= size(hist%xred,2))then
320    write(message, '(5a)' )&
321 &      'The number of atoms in the hist file does not correspond to the supercell.',ch10,&
322 &      'You should call the routine fit_polynomial_coeff_mapHistToRef before',ch10,&
323 &      'Action: Contact abinit group'
324    ABI_BUG(message)
325  end if
326 
327 !Allocation of temporary arrays
328  ABI_MALLOC(displacement,(3,natom,ntime))
329  ABI_MALLOC(du_delta,(6,3,natom,ntime))
330  ABI_MALLOC(energy_diff,(ntime))
331  ABI_MALLOC(fcart_fixed,(3,natom,ntime))
332  ABI_MALLOC(fcart_diff,(3,natom,ntime))
333  ABI_MALLOC(gred_fixed,(3,natom,ntime))
334  ABI_MALLOC(strain,(6,ntime))
335  ABI_MALLOC(strten_fixed,(6,ntime))
336  ABI_MALLOC(strten_diff,(6,ntime))
337  ABI_MALLOC(sqomega,(ntime))
338  ABI_MALLOC(ucvol,(ntime))
339 
340  displacement = zero 
341  du_delta = zero 
342  strain = zero; 
343  fcart_fixed  = zero 
344  gred_fixed  = zero
345  strain = zero 
346  strten_fixed = zero 
347  strten_diff = zero
348  sqomega = zero 
349  ucvol = zero
350 
351  do itime=1,ntime
352 !  Get strain
353    call strain_get(strain_t,rprim=eff_pot%supercell%rprimd,&
354 &                  rprim_def=hist%rprimd(:,:,itime),symmetrized=.FALSE.)
355    if (strain_t%name /= "reference")  then
356      do ii=1,3
357        strain(ii,itime) = strain_t%strain(ii,ii)
358      end do
359      strain(4,itime) = (strain_t%strain(2,3) + strain_t%strain(3,2))
360      strain(5,itime) = (strain_t%strain(3,1) + strain_t%strain(1,3))
361      strain(6,itime) = (strain_t%strain(2,1) + strain_t%strain(1,2))
362    else
363      strain(:,itime) = zero
364    end if
365 
366 !  Get displacement and du_delta
367    call effective_potential_getDisp(displacement(:,:,itime),du_delta(:,:,:,itime),natom,&
368 &                                   hist%rprimd(:,:,itime),eff_pot%supercell%rprimd,comm,&
369 &                                   xred_hist=hist%xred(:,:,itime),xcart_ref=eff_pot%supercell%xcart,&
370 &                                   compute_displacement=.TRUE.,compute_duDelta=.TRUE.)
371 
372 !  Get forces and stresses from harmonic part (fixed part)     
373    call effective_potential_evaluate(eff_pot,energy,fcart_fixed(:,:,itime),gred_fixed(:,:,itime),&
374 &                                    strten_fixed(:,itime),natom,hist%rprimd(:,:,itime),&
375 &                                    displacement=displacement(:,:,itime),&
376 &                                    du_delta=du_delta(:,:,:,itime),strain=strain(:,itime),&
377 &                                    compute_anharmonic=.true.,verbose=.FALSE.)
378    
379 !  Compute \Omega^{2} and ucvol for each time
380    call metric(gmet,gprimd,-1,rmet,hist%rprimd(:,:,itime),ucvol(itime))
381 !  Formula: sqomega(itime) = (((ucvol(itime)**(-2.))* ((natom)**(0.5)))**(-1.0/3.0))**2
382 !   Compact form:
383    sqomega(itime) = ((ucvol(itime)**(4.0/3.0)) / ((natom)**(1/3.0)))
384 
385 !  Compute the difference between History and model (fixed part)
386    fcart_diff(:,:,itime) =  hist%fcart(:,:,itime) - fcart_fixed(:,:,itime)
387    energy_diff(itime)    =  hist%etot(itime) - energy
388    strten_diff(:,itime)  =  hist%strten(:,itime) - strten_fixed(:,itime)
389  end do ! End Loop itime 
390    
391 !Set the training set
392  call training_set_init(ts,displacement,du_delta,natom,ntime,strain,sqomega,ucvol)
393 !Set the fit_data
394  call fit_data_init(fit_data,energy_diff,fcart_diff,natom,ntime,strten_diff,ts)
395 
396 !Free space
397  call training_set_free(ts)
398  ABI_FREE(displacement)
399  ABI_FREE(du_delta)
400  ABI_FREE(energy_diff)
401  ABI_FREE(fcart_fixed)
402  ABI_FREE(fcart_diff)
403  ABI_FREE(gred_fixed)
404  ABI_FREE(strain)
405  ABI_FREE(strten_fixed)
406  ABI_FREE(strten_diff)
407  ABI_FREE(sqomega)
408  ABI_FREE(ucvol)
409 
410 end subroutine fit_data_compute

m_fit_data/fit_data_free [ Functions ]

[ Top ] [ m_fit_data ] [ Functions ]

NAME

 fit_data_free

FUNCTION

 Free the fit_data datatype

INPUTS

 fit_data<fit_data_type> = fit_data to be free

OUTPUT

SOURCE

224 subroutine fit_data_free(fit_data)
225 
226  implicit none
227   
228 !Arguments ------------------------------------
229 !scalars
230 !arrays
231  type(fit_data_type),intent(inout) :: fit_data
232 !Local variables-------------------------------
233 !scalar
234 !arrays
235 ! *************************************************************************
236 
237 ! Reset integer values
238   fit_data%ntime = 0
239   fit_data%natom = 0
240 
241 ! Deallocate arrays  
242   if(allocated(fit_data%energy_diff)) then
243     ABI_FREE(fit_data%energy_diff)
244   end if
245   if(allocated(fit_data%fcart_diff)) then
246     ABI_FREE(fit_data%fcart_diff)
247   end if
248   if(allocated(fit_data%strten_diff)) then
249     ABI_FREE(fit_data%strten_diff)
250   end if
251   call training_set_free(fit_data%training_set)
252    
253 end subroutine fit_data_free

m_fit_data/fit_data_init [ Functions ]

[ Top ] [ m_fit_data ] [ Functions ]

NAME

 fit_data_init

FUNCTION

 Initialize fit_data datatype

INPUTS

 energy_diff(3,natom,ntime) = Difference of energy between DFT calculation and 
                             fixed part of the model (more often harmonic part)
 fcart_diff(3,natom,ntime) = Difference of cartesian forces between DFT calculation and 
                             fixed part of the model (more often harmonic part)
 natom = Number of atoms
 ntime = Number of time (number of snapshot, number of md step...)
 strten_diff(6,natom) = Difference of stress tensor between DFT calculation and 
                        fixed part of the model (more often harmonic part)
 sqomega(ntime) =  Sheppard and al Factors \Omega^{2} see J.Chem Phys 136, 074103 (2012) [[cite:Sheppard2012]]
 ucvol(ntime) = Volume of the system for each time
 ts<training_set_type> = datatype with the information about the training set

OUTPUT

 fit_data<fit_data_type> = fit_data datatype to be initialized

SOURCE

159 subroutine fit_data_init(fit_data,energy_diff,fcart_diff,natom,ntime,strten_diff,ts)
160 
161 !Arguments ------------------------------------
162 !scalars
163  integer,intent(in) :: natom,ntime
164 !arrays
165  real(dp),intent(in) :: energy_diff(ntime),fcart_diff(3,natom,ntime)
166  real(dp),intent(in) :: strten_diff(6,ntime)
167  type(training_set_type),intent(in) :: ts
168  type(fit_data_type),intent(inout) :: fit_data
169 !Local variables-------------------------------
170 !scalar
171 !arrays
172  character(len=500) :: message
173 ! *************************************************************************
174 
175  if(natom /= ts%natom)then
176    write(message, '(a)')&
177 &      ' The number of atoms does not correspond to the training set'
178    ABI_BUG(message)
179  end if
180 
181  if(ntime /= ts%ntime)then
182    write(message, '(a)')&
183 &      ' The number of time does not correspond to the training set'
184    ABI_BUG(message)
185  end if
186  
187 !Free the output 
188  call fit_data_free(fit_data)
189 
190 !Set integer values 
191  fit_data%ntime = ntime
192  fit_data%natom = natom
193 
194 !allocate arrays
195  ABI_MALLOC(fit_data%fcart_diff,(3,natom,ntime))
196  fit_data%fcart_diff(:,:,:) = fcart_diff(:,:,:)
197  
198  ABI_MALLOC(fit_data%strten_diff,(6,ntime))
199  fit_data%strten_diff(:,:) = strten_diff(:,:)
200 
201  ABI_MALLOC(fit_data%energy_diff,(ntime))
202  fit_data%energy_diff(:) = energy_diff
203  
204  call training_set_init(fit_data%training_set,ts%displacement,ts%du_delta,&
205 &                       natom,ntime,ts%strain,ts%sqomega,ts%ucvol)
206  
207 end subroutine fit_data_init

m_fit_data/fit_data_type [ Types ]

[ Top ] [ m_fit_data ] [ Types ]

NAME

 fit_data_type

FUNCTION

SOURCE

 97  type, public :: fit_data_type
 98 
 99    integer :: ntime
100 !   Number of time in the training set
101    
102    integer :: natom
103 !   Number of atoms in the training set
104 
105    real(dp),allocatable :: energy_diff(:)
106 !   energy(ntime)
107 !   Array with the diffence between energy from training set and energy from initial model.
108 !   The model constains only harmonic part
109 
110    real(dp),allocatable :: fcart_diff(:,:,:)
111 !   fcart_diff(3,natom,ntime)
112 !   Array with the diffence between cartesian forces from training set and forces from initial model.
113 !   The model constains only harmonic part
114 
115    real(dp),allocatable :: strten_diff(:,:)
116 !   strten_diff(6,ntime)
117 !   Array with the diffence between strain from training set and strain from initial model.
118 !   The model constains only harmonic part
119 
120    type(training_set_type) :: training_set
121 !    datatype with the information of the training set
122    
123  end type fit_data_type
124 
125 !routine for fit_data
126  public :: fit_data_compute
127  public :: fit_data_init
128  public :: fit_data_free

m_fit_data/training_set_free [ Functions ]

[ Top ] [ m_fit_data ] [ Functions ]

NAME

 training_set_free

FUNCTION

 Free the training_set datatype

INPUTS

 training_set<training_set_type> = training_set to be free

OUTPUT

SOURCE

492 subroutine training_set_free(ts)
493 
494  implicit none
495   
496 !Arguments ------------------------------------
497 !scalars
498 !arrays
499  type(training_set_type),intent(inout) :: ts  
500 !Local variables-------------------------------
501 !scalar
502 !arrays
503 ! *************************************************************************
504 
505 ! Reset integer values
506   ts%ntime = 0
507   ts%natom = 0
508 
509 ! Deallocate arrays  
510   if(allocated(ts%displacement)) then
511     ABI_FREE(ts%displacement)
512   end if
513   if(allocated(ts%du_delta)) then
514     ABI_FREE(ts%du_delta)
515   end if
516   if(allocated(ts%strain)) then
517     ABI_FREE(ts%strain)
518   end if
519   if(allocated(ts%sqomega))then
520     ABI_FREE(ts%sqomega)
521   end if
522   if(allocated(ts%ucvol)) then
523     ABI_FREE(ts%ucvol)
524   end if
525    
526 end subroutine training_set_free

m_fit_data/training_set_init [ Functions ]

[ Top ] [ m_fit_data ] [ Functions ]

NAME

 training_set_init

FUNCTION

 Initialize training_set datatype

INPUTS

 du_delta(6,3,natom,ntime)  = Variation to displacements wrt to the strain (Bohr)
 displacement(3,natom,ntime)= Atomic displacement wrt to the reference (Bohr)
 natom = number of atoms
 ntime = number of time step
 strain(6,ntime) = Strain
 sqomega =  Sheppard and al Factors \Omega^{2} see J.Chem Phys 136, 074103 (2012) [[cite:Sheppard2012]]
 ucvol(ntime) = Volume of the supercell for each time (Bohr^3)

OUTPUT

 ts<training_set_type> = training set to be initialized

SOURCE

438 subroutine training_set_init(ts,displacement,du_delta,natom,ntime,strain,sqomega,ucvol)
439 
440 !Arguments ------------------------------------
441 !scalars
442  integer,intent(in) :: natom,ntime
443 !arrays
444  real(dp),intent(in) :: displacement(3,natom,ntime),du_delta(6,3,natom,ntime)
445  real(dp),intent(in) :: strain(6,ntime),sqomega(ntime),ucvol(ntime)
446  type(training_set_type),intent(inout) :: ts  
447 !Local variables-------------------------------
448 !scalar
449 !arrays
450 ! *************************************************************************
451 
452 !Free the output 
453  call training_set_free(ts)
454 
455 !Set integer values 
456  ts%ntime = ntime
457  ts%natom = natom
458 
459 !allocate arrays
460  ABI_MALLOC(ts%displacement,(3,natom,ntime))
461  ts%displacement(:,:,:) = displacement(:,:,:)
462  
463  ABI_MALLOC(ts%du_delta,(6,3,natom,ntime))
464  ts%du_delta(:,:,:,:) = du_delta(:,:,:,:)
465  
466  ABI_MALLOC(ts%strain,(6,ntime))
467  ts%strain(:,:) = strain(:,:)
468  
469  ABI_MALLOC(ts%sqomega,(ntime))
470  ts%sqomega(:) = sqomega(:)
471  
472  ABI_MALLOC(ts%ucvol,(ntime))
473  ts%ucvol(:) = ucvol(:)
474  
475 end subroutine training_set_init

m_fit_data/training_set_type [ Types ]

[ Top ] [ m_fit_data ] [ Types ]

NAME

 training_set_type

FUNCTION

 datatype for with all the information for the fit process
 This structure contains all the information of the training set:
   - ntime
   - displacement
   - du_delta
   - strain
   - sqomega
   - ucvol

SOURCE

51  type, public :: training_set_type
52 
53    integer :: ntime
54 !    Number of time in the training set
55    
56    integer :: natom
57 !    Number of atoms in the training set
58    
59    real(dp), allocatable :: displacement(:,:,:)
60 !    displacement(3,natom,ntime)
61 !    displacement array, difference of the position in cartisian coordinates
62 !    between training set and reference
63 
64    real(dp), allocatable :: du_delta(:,:,:,:)
65 !    du_delta(6,3,natom,ntime)
66 !    du_delta array, variation of displacement wrt to the strain
67 
68    real(dp), allocatable :: strain(:,:)
69 !    strain(6,ntime)
70 !    strain array, strain in the training set
71 
72    real(dp), allocatable :: sqomega(:)
73 !    sqomega(ntime)
74 !    sqomega(itime) = (((ucvol(itime)**(-2.))* ((natom_sc)**(0.5)))**(-1.0/3.0))**2
75 
76    real(dp), allocatable :: ucvol(:)
77 !    ucvol(ntime)
78 !    ucvol array, volume of the cell in the training set
79 
80  end type training_set_type
81  
82 !routine for training_set
83  public :: training_set_init
84  public :: training_set_free