-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathPhonon.c
1170 lines (976 loc) · 38.5 KB
/
Phonon.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/** ***************************************************** **/
/** ** Phonon Vibration Analysis ** **/
/** **/
/** ** Version 2 ** **/
/** **/
/** By: Pedro Brandimarte ([email protected]) and **/
/** Alexandre Reily Rocha ([email protected]) **/
/** **/
/** ***************************************************** **/
/** Implementation of phonon analysis: **/
/** - reads the output data from a siesta force **/
/** constants (FC) calculation runned with the script **/
/** 'runFC.sh'; **/
/** - builds the force constants matrix and computes the **/
/** phonon frequencies and modes by finite differences; **/
/** - computes the Hamiltonian and overlap matrices **/
/** derivatives with respect to the dynamic atoms **/
/** displacements and apply suitable corrections; **/
/** - calculates the electron-phonon coupling matrix. **/
/** ***************************************************** **/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "Extern.h"
#include "Check.h"
#include "Utils.h"
#include "Phonon.h"
/* Structure for atomic number and mass. */
typedef struct ATNMASS nmass;
struct ATNMASS {
int Z; /* atomic number */
double A; /* atomic mass */
};
/* Structure for chemical element info. */
typedef struct CHEMIC element;
struct CHEMIC {
int id; /* number of the atom at system structure */
nmass atom; /* atomic number and mass */
};
/* Structure for 'xyz' coordinates. */
typedef struct ATCOORD xyzcoord;
struct ATCOORD {
char name[2]; /* element specie */
double x; /* x coordinate */
double y; /* y coordinate */
double z; /* z coordinate */
};
static char *workDir; /* work directory */
static char *FCdir; /* FC directory */
static char sysLabel[30]; /* system label */
static int nAtoms; /* number of atoms */
static int nspin; /* spin polarization */
static int FCfirst; /* first dynamic atom */
static int FClast; /* last dynamic atom */
static int nDyn; /* number of dynamic atoms */
static int no_u; /* number of basis orbitals from unit cell */
static int *orbIdx; /* first orbital index of each atom. */
static double FCdispl; /* atoms displacement */
static double *ef; /* Fermi energy values */
static element *dynAtoms; /* dynamic atoms chemical info */
static nmass periodicTable[95] = { /* {Z,A} - from SIESTA 3.1 */
{ 0, 0.00},{ 1, 1.01},{ 2, 4.00},{ 3, 6.94},{ 4, 9.01},
{ 5, 10.81},{ 6, 12.01},{ 7, 14.01},{ 8, 16.00},{ 9, 19.00},
{10, 20.18},{11, 22.99},{12, 24.31},{13, 26.98},{14, 28.09},
{15, 30.97},{16, 32.07},{17, 35.45},{18, 39.95},{19, 39.10},
{20, 40.08},{21, 44.96},{22, 47.88},{23, 50.94},{24, 52.00},
{25, 54.94},{26, 55.85},{27, 58.93},{28, 58.69},{29, 63.55},
{30, 65.39},{31, 69.72},{32, 72.61},{33, 74.92},{34, 78.96},
{35, 79.90},{36, 83.80},{37, 85.47},{38, 87.62},{39, 88.91},
{40, 91.22},{41, 92.91},{42, 95.94},{43, 98.91},{44,101.07},
{45,102.91},{46,106.42},{47,107.87},{48,112.41},{49,114.82},
{50,118.71},{51,121.75},{52,127.60},{53,126.90},{54,131.29},
{55,132.91},{56,137.33},{57,138.91},{58,140.12},{59,140.91},
{60,144.24},{61,146.92},{62,150.36},{63,151.97},{64,157.25},
{65,158.93},{66,162.50},{67,164.93},{68,167.26},{69,168.93},
{70,173.04},{71,174.97},{72,178.49},{73,180.95},{74,183.85},
{75,186.21},{76,190.20},{77,192.22},{78,195.08},{79,196.97},
{80,200.59},{81,204.38},{82,207.20},{83,208.98},{84,208.98},
{85,209.99},{86,222.02},{87,223.02},{88,226.03},{89,227.03},
{90,232.04},{91,231.04},{92,238.03},{93,237.05},{94,244.06}
};
/* ********************************************************* */
/* Reads the file 'inputFC.in' and assigns static global */
/* variables. */
static void assignGlobalVar ()
{
register int i, j, len;
int nSpecies;
element *species;
char FCdisplUnit[5]; /* unit of the displacement */
char **name; /* element name */
char *inputFile;
FILE *FCinfo;
/* Sets the file name 'inputFC.in' with work directory path. */
len = strlen (workDir);
inputFile = CHECKmalloc ((len + 11) * sizeof (char));
sprintf (inputFile, "%sinputFC.in", workDir);
/* Opens the file with FC run informations. */
FCinfo = CHECKfopen (inputFile, "r");
/* Reads and assigns global variables. */
CHECKfscanf (fscanf (FCinfo, "%s", sysLabel), inputFile);
printf (" System label:\t\t\t%s\n", sysLabel);
CHECKfscanf (fscanf (FCinfo, "%d", &nAtoms), inputFile);
printf (" Number of atoms:\t\t\t%d\n", nAtoms);
/* Different species from the system. */
CHECKfscanf (fscanf (FCinfo, "%d", &nSpecies), inputFile);
printf (" Different system species:\t\t%d\n", nSpecies);
species = CHECKmalloc (nSpecies * sizeof (element));
name = CHECKmalloc (nSpecies * sizeof (*name));
for (i = 0; i < nSpecies; i++) {
CHECKfscanf (fscanf (FCinfo, "%d", &species[i].id), inputFile);
CHECKfscanf (fscanf (FCinfo, "%d", &species[i].atom.Z), inputFile);
name[i] = CHECKmalloc (10 * sizeof (char));
CHECKfscanf (fscanf (FCinfo, "%s", name[i]), inputFile);
printf ("\t\t\t\t\t %d %d %s\n", species[i].id,
species[i].atom.Z, name[i]);
}
CHECKfscanf (fscanf (FCinfo, "%d", &nspin), inputFile);
printf (" Spin polarization (1 or 2):\t\t%d\n", nspin);
CHECKfscanf (fscanf (FCinfo, "%d", &FCfirst), inputFile);
printf (" First dynamic atom:\t\t\t%d\n", FCfirst);
CHECKfscanf (fscanf (FCinfo, "%d", &FClast), inputFile);
printf (" Last dynamic atom:\t\t\t%d\n", FClast);
nDyn = FClast - FCfirst + 1;
printf (" Number of dynamic atoms:\t\t%d\n", nDyn);
CHECKfscanf (fscanf (FCinfo, "%lf", &FCdispl), inputFile);
CHECKfscanf (fscanf (FCinfo, "%s", FCdisplUnit), inputFile);
if (strcmp (FCdisplUnit, "bohr") == 0) {
FCdispl = bohr2ang * FCdispl;
}
else if (strcmp (FCdisplUnit, "ang") != 0) {
fprintf (stderr,
"\n ERROR: unrecognized displacement unit \"%s\" at FC\n",
FCdisplUnit);
fprintf (stderr,
" fdf input file! It must be \"Ang\" or \"Bohr\"!");
fprintf (stderr, "\n\n");
exit (EXIT_FAILURE);
}
printf (" Atoms displacement:\t\t\t%.5f (ang)\n", FCdispl);
/* Species of the dynamic atoms. */
printf (" Dynamic atoms species:\n");
dynAtoms = CHECKmalloc (nDyn * sizeof (element));
for (i = 0; i < nDyn; i++)
CHECKfscanf (fscanf (FCinfo, "%d", &dynAtoms[i].id), inputFile);
for (i = 0; i < nDyn; i++)
for (j = 0; j < nSpecies; j++) {
/* Searches the correspondent atom specie. */
if (dynAtoms[i].id == species[j].id) {
dynAtoms[i].id = FCfirst + i;
dynAtoms[i].atom.Z = species[j].atom.Z;
dynAtoms[i].atom.A = periodicTable[dynAtoms[i].atom.Z].A;
printf ("\t\t\t\t\t%d %d %.2f %s\n", dynAtoms[i].id,
dynAtoms[i].atom.Z, dynAtoms[i].atom.A, name[j]);
break ;
}
}
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Closes the file 'inputFC.in'. */
CHECKfclose (fclose (FCinfo), inputFile);
/* Frees memory. */
free (inputFile);
free (species);
for (i = 0; i < nSpecies; i++)
free (name[i]);
free (name);
} /* assignGlobalVar */
/* ********************************************************* */
/* Reads at '.ef' file the Fermi energy from the undisplaced */
/* system and the Fermi energy obtained after each */
/* displacement. */
static void readFermiEnergy ()
{
register int i, len;
char *efFile;
FILE *EF;
/* Sets the '.ef' file name with 'FCdir' path. */
len = strlen (FCdir);
len += strlen (sysLabel);
efFile = CHECKmalloc ((len + 4) * sizeof (char));
efFile[0] = '\0';
sprintf (efFile, "%s%s.ef", FCdir, sysLabel);
/* Opens the '.ef' file. */
printf ("\n reading \"%s\" file... ", efFile);
EF = CHECKfopen (efFile, "r");
/* Reads the Fermi energies. */
ef = UTILdoubleVector (6 * nDyn + 1);
for (i = 0; i < 6 * nDyn + 1; i++)
CHECKfscanf (fscanf (EF, "%*d %lf", &ef[i]), efFile);
/* Closes the file. */
CHECKfclose (fclose (EF), efFile);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Frees memory. */
free (efFile);
} /* readFermiEnergy */
/* ********************************************************* */
/* Reads the first orbital index of each atom in the unit */
/* cell from the '.orb' file. */
static void readOrbitalIndex ()
{
register int i, len;
char *orbFile;
FILE *ORB;
/* Sets the '.orb' file name with 'FCdir' path. */
len = strlen (FCdir);
len += strlen (sysLabel);
orbFile = CHECKmalloc ((len + 5) * sizeof (char));
orbFile[0] = '\0';
sprintf (orbFile, "%s%s.orb", FCdir, sysLabel);
/* Opens the '.orb' file. */
printf ("\n reading \"%s\" file... ", orbFile);
ORB = CHECKfopen (orbFile, "r");
/* Reads the first orbital index of each atom. */
orbIdx = CHECKmalloc ((nAtoms + 1) * sizeof (int));
for (i = 0; i < nAtoms + 1; i++)
CHECKfscanf (fscanf (ORB, "%d", &orbIdx[i]), orbFile);
/* Closes the file. */
CHECKfclose (fclose (ORB), orbFile);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Number of basis orbitals from unit cell. */
no_u = orbIdx[nAtoms];
printf ("\n Basis orbitals per unit cell:\t\t%d\n", no_u);
/* First orbital of the first dynamic atom. */
printf (" First orbital from dynamic atom:\t\t%d\n",
orbIdx[FCfirst-1] + 1);
/* Dynamic atoms orbitals quantity. */
printf (" Number of dynamic atoms basis orbitals:\t%d\n",
orbIdx[FClast] - orbIdx[FCfirst-1]);
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Frees memory. */
free (orbFile);
} /* readOrbitalIndex */
/* ********************************************************* */
/* Runs a script that collects required informations from FC */
/* input 'fdf' file and writes them at 'inputFC.in' file. */
/* Calls 'assignGlobalVar' function to assign global */
/* variables. */
void PHONreadFCfdf (char *exec, char *FCpath, char *FCinput,
int calcType, char *FCsplit, int *nDynTot,
int *nDynOrb, int *spinPol)
{
register int i, len;
char calc[2];
char *scriptCall;
/* For calling the script, one should use a string */
/* like this: "[script name with path] [FC directory]" */
len = strlen(FCpath) + strlen(FCinput) + strlen(FCsplit);
scriptCall = CHECKmalloc ((len + 19) * sizeof (char));
scriptCall[0] = '\0';
calc[0] = '\0';
sprintf(&calc[0], "%d", calcType);
strcpy (scriptCall, "setInput.sh ");
strcat (scriptCall, FCpath);
strcat (scriptCall, " ");
strcat (scriptCall, FCinput);
strcat (scriptCall, " ");
strcat (scriptCall, calc);
strcat (scriptCall, " ");
strcat (scriptCall, FCsplit);
/* Assigns the work directory global variable. */
len = strlen (exec);
workDir = CHECKmalloc ((len - 9) * sizeof (char));
for (i = 0; i < len - 10; i++)
workDir[i] = exec[i];
workDir[i] = '\0';
/* Assigns the force constants directory global variable. */
len = strlen (FCpath);
if (FCpath[len - 1] == '/') {
FCdir = CHECKmalloc ((len + 1) * sizeof (char));
strcpy (FCdir, FCpath);
}
else {
FCdir = CHECKmalloc ((len + 2) * sizeof (char));
strcpy (FCdir, FCpath);
FCdir[len] = '/';
FCdir[len + 1] = '\0';
}
/* Runs the script that collects required informations from */
/* the input 'fdf' file and puts at 'inputFC.in' file. */
i = system (scriptCall);
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
if (i != 0) {
fprintf (stderr, " ERROR: problem when trying to run");
fprintf (stderr, " 'setInput.sh' script!\n\n");
exit (EXIT_FAILURE);
}
/* Reads the file 'inputFC.in' and assigns global variables. */
assignGlobalVar ();
if (calcType == 1) { /* 'full' calculation */
/* Reads the Fermi energies. */
printf ("\n Gets Fermi energies from (un)displaced systems:\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
readFermiEnergy ();
/* Gets the first orbital index of each atom. */
printf ("\n Gets basis orbitals dimensions info:\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
readOrbitalIndex ();
/* Returns the total number of orbitals for 'e-ph' coupling matrix. */
*nDynOrb = orbIdx[FClast] - orbIdx[FCfirst-1];
}
/* Returns the dimension of 'FC' matrix. */
*nDynTot = 3 * nDyn;
*spinPol = nspin;
/* Removes 'inputFC.in' file. */
scriptCall[0] = '\0';
strcpy (scriptCall, "rm ");
strcat (scriptCall, exec);
scriptCall[strlen (scriptCall)-10] = '\0'; /* removes 'exec' */
strcat (scriptCall, "inputFC.in");
i = system (scriptCall);
/* Frees memory. */
free (scriptCall);
} /* PHONreadFCfdf */
/* ********************************************************* */
/* Removes egg-box effect by imposing force conservation. */
static void rmEggBox (double *fullFCM)
{
register int i, j, k, dyn;
double sum;
for (j = 0; j < 3 * nDyn; j++) {
dyn = FCfirst - 1 + j / 3; /* dynamic atom */
for (k = 0; k < 3; k++) { /* coordinates (x,y,z) */
fullFCM[idx(dyn*3+k,j,3*nAtoms)] = 0.0;
sum = 0.0;
for (i = 0; i < nAtoms; i++) /* sum over all atoms coord 'k' */
sum = sum + fullFCM[idx(i*3+k,j,3*nAtoms)];
fullFCM[idx(dyn*3+k,j,3*nAtoms)] = - 1.0 * sum;
}
}
} /* rmEggBox */
/* ********************************************************* */
/* Symmetrizes and mass-scales the 'FC' matrix. */
static void symmetrizesAndMassScale (double *FC)
{
register int i, j;
double aux;
for (j = 0; j < 3 * nDyn; j++)
for (i = j; i < 3 * nDyn; i++) {
/* Computes the mean. */
aux = (FC[idx(i,j,3*nDyn)] + FC[idx(j,i,3*nDyn)]) / 2.0;
/* Mass-scales. */
aux = aux / sqrt (dynAtoms[i/3].atom.A * dynAtoms[j/3].atom.A);
/* Simetrizes. */
FC[idx(i,j,3*nDyn)] = FC[idx(j,i,3*nDyn)] = aux;
}
} /* symmetrizesAndMassScale */
/* ********************************************************* */
/* Reads the SIESTA force constants matrix and computes */
/* phonon modes and frequencies with finite differences. */
void PHONfreq (double *EigVec, double *EigVal)
{
register int i, j, len;
double cst;
double *fullFCneg, *fullFCpos;
char check[25];
char *FCMfile;
FILE *FCM;
/* Sets the SIESTA FC matrix file name with 'FCdir' path. */
len = strlen (FCdir);
len += strlen (sysLabel);
FCMfile = CHECKmalloc ((len + 4) * sizeof (char));
sprintf (FCMfile, "%s%s.FC", FCdir, sysLabel);
/* Opens the SIESTA FC matrix file. */
printf ("\n Reading %s file... ", FCMfile);
FCM = CHECKfopen (FCMfile, "r");
/* Checks if the file starts correctly. */
if ((fgets(check,24,FCM)==NULL) ||
(strncmp(check,"Force constants matrix",22)!=0)) {
fprintf (stderr,
" ERROR: the file %s is not written correctly!\n\n",
FCMfile);
exit (EXIT_FAILURE);
}
/* FC matrix with all atoms */
/* [negative (minus) and positive (plus) displacement]. */
fullFCneg = CHECKmalloc (3 * nAtoms * 3 * nDyn * sizeof (double));
fullFCpos = CHECKmalloc (3 * nAtoms * 3 * nDyn * sizeof (double));
/* Reads the SIESTA FC matrix file */
/* (obs.: matrix in column-major order). */
for (j = 0; j < 3 * nDyn; j++) {
/* Negative displacement. */
for (i = 0; i < 3 * nAtoms; i++)
CHECKfscanf (fscanf (FCM, "%lE",
&fullFCneg[idx(i,j,3*nAtoms)]), FCMfile);
/* Positive displacement. */
for (i = 0; i < 3 * nAtoms; i++)
CHECKfscanf (fscanf (FCM, "%lE",
&fullFCpos[idx(i,j,3*nAtoms)]), FCMfile);
}
/* Closes the SIESTA FC matrix file. */
CHECKfclose (fclose (FCM), FCMfile);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Removes egg-box effect. */
printf ("\n Removing egg-box effect... ");
rmEggBox (fullFCneg);
rmEggBox (fullFCpos);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* The SIESTA FC matrix file contains the values of force */
/* by displacement [eV/Ang^2]. In order to compute the */
/* Hessian (force constants matrix) with finite differences, */
/* one has only to subtract the value corresponding to the */
/* negative displacement by the value corresponding to the */
/* positive displacement and divide by 2. */
printf ("\n Reducing to dynamic atoms dimension");
printf (" and computing finite differences... ");
len = (FCfirst - 1) * 3;
for (j = 0; j < 3 * nDyn; j++)
for (i = len; i < FClast * 3; i++)
EigVec[idx(i-len,j,3*nDyn)] =
(fullFCneg[idx(i,j,3*nAtoms)] +
fullFCpos[idx(i,j,3*nAtoms)]) / 2.0;
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Symmetrizes and mass-scales the matrix. */
printf ("\n \"Symmetrizing\" and mass-scaling the FC matrix... ");
symmetrizesAndMassScale (EigVec);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Prints on screen the reduced, */
/* mass-scaled and symmetrized FC matrix. */
printf ("\n Reduced force constants matrix:\n\n");
for (i = 0; i < 3 * nDyn; i++) {
for (j = 0; j < 3 * nDyn; j++)
printf (" % .5e ", EigVec[idx(i,j,3*nDyn)]);
printf ("\n");
}
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Computes all eigenvalues and eigenvectors. */
CHECKdsyevd (3 * nDyn, EigVec, EigVal);
/* Prints on screen the phonon energies. */
printf ("\n Phonon energies (eV):\n\n");
cst = hbar * sqrt (1.0e20 * eV2joule / amu2kg);
for (i = 0; i < 3 * nDyn; i++) {
if (EigVal[i] < 0.0) {
printf (" %d % .5e\n", i + 1, - cst * sqrt(-EigVal[i]));
EigVal[i] = 0.0;
} else {
EigVal[i] = cst * sqrt(EigVal[i]);
printf (" %d % .5e\n", i + 1, EigVal[i]);
}
}
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Prints on screen the phonon modes. */
printf ("\n Normalized phonon modes (Ang*amu^0.5):\n\n");
for (i = 0; i < 3 * nDyn; i++)
printf (" %7d ", i+1);
printf ("\n");
for (i = 0; i < 3 * nDyn; i++) {
for (j = 0; j < 3 * nDyn; j++)
printf (" % .5e ", EigVec[idx(i,j,3*nDyn)]);
printf ("\n");
}
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Frees memory. */
free (fullFCneg);
free (fullFCpos);
free (FCMfile);
} /* PHONfreq */
/* ********************************************************* */
/* Reads the SIESTA 'xyz' file and write 'xyz's files for */
/* each computed phonon mode. */
void PHONjmolVib (double *EigVec)
{
register int i, j, k, len;
int aux;
xyzcoord *coord;
char *XYZfile, *JMOLfile;
FILE *XYZ, *JMOL;
/* Sets the SIESTA 'xyz' file name with 'FCdir' path. */
len = strlen (FCdir);
len += strlen (sysLabel);
XYZfile = CHECKmalloc ((len + 5) * sizeof (char));
sprintf (XYZfile, "%s%s.xyz", FCdir, sysLabel);
/* Opens the SIESTA 'xyz' file. */
printf ("\n Reading %s file... ", XYZfile);
XYZ = CHECKfopen (XYZfile, "r");
/* Checks if the file starts correctly. */
CHECKfscanf (fscanf (XYZ, "%d", &aux), XYZfile);
if (aux != nAtoms) {
fprintf (stderr,
" ERROR: the file %s is not written correctly!\n\n",
XYZfile);
exit (EXIT_FAILURE);
}
/* Allocs structure for atomic species and coordinates. */
coord = CHECKmalloc (nAtoms * sizeof (xyzcoord));
/* Reads the SIESTA 'xyz' file. */
for (i = 0; i < nAtoms; i++)
CHECKfscanf (fscanf (XYZ, "%s %le %le %le",
coord[i].name, &coord[i].x,
&coord[i].y, &coord[i].z), XYZfile);
/* Closes the SIESTA 'xyz' file. */
CHECKfclose (fclose (XYZ), XYZfile);
printf ("ok!\n\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Sets the path for the output Jmol files. */
len = strlen (workDir);
len += strlen (sysLabel);
JMOLfile = CHECKmalloc ((len + 12) * sizeof (char));
for (i = 0, j = 1; i < 3*nDyn; i++) {
/* Opens the JMOL 'xyz' output file. */
sprintf (JMOLfile, "%s%sJMOL%d.xyz", workDir, sysLabel, j);
printf (" Writing %s file... ", JMOLfile);
JMOL = CHECKfopen (JMOLfile, "w");
fprintf (JMOL, " %d\n\n", nAtoms);
/* Writes only the coordinates. */
for (k = 0; k < FCfirst - 1; k++)
fprintf (JMOL, "%s\t% e\t% e\t% e\n", coord[k].name,
coord[k].x, coord[k].y, coord[k].z);
/* Writes the coordinates and the normalized phonon mode. */
for (k = FCfirst - 1; k < FClast; k++)
fprintf (JMOL, "%s\t% e\t% e\t% e\t% e\t% e\t% e\n",
coord[k].name, coord[k].x, coord[k].y, coord[k].z,
EigVec[idx(3*(k-FCfirst+1),i,3*nDyn)],
EigVec[idx(3*(k-FCfirst+1)+1,i,3*nDyn)],
EigVec[idx(3*(k-FCfirst+1)+2,i,3*nDyn)]);
/* Writes only the coordinates. */
for (k = FClast; k < nAtoms; k++)
fprintf (JMOL, "%s\t% e\t% e\t% e\n", coord[k].name,
coord[k].x, coord[k].y, coord[k].z);
/* Closes the JMOL 'xyz' output file. */
CHECKfclose (fclose (JMOL), JMOLfile);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
j++;
} /* for (i = 0, j = 1; ... */
/* Frees memory. */
free (coord);
free (XYZfile);
free (JMOLfile);
} /* PHONjmolVib */
/* ********************************************************* */
/* Reads the Hamiltonian and the overlap matrices from */
/* '.gHS' file. */
static void readHSfile (char *HSfile, double *H, double *S, int efIdx)
{
register int i, j, k, s, foo;
int CKno_u, CKnspin, maxnhtot;
double *Hsparse, *Ssparse;
int *numh, *listh;
FILE *gHS;
/* Opens the '.gHS' binary file. */
printf (" reading \"%s\" file... ", HSfile);
gHS = CHECKfopen (HSfile, "rb");
/* Reads matrices dimensions and checks file consistency. */
fseek (gHS, 0L, SEEK_SET);
CHECKfread (fread (&CKno_u, sizeof (int), 1, gHS), 1, HSfile);
CHECKfread (fread (&CKnspin, sizeof (int), 1, gHS), 1, HSfile);
CHECKfread (fread (&maxnhtot, sizeof (int), 1, gHS), 1, HSfile);
if ((CKno_u != no_u) || (CKnspin != nspin)) {
fprintf (stderr,
" ERROR: the file %s is not written correctly!\n\n",
HSfile);
exit (EXIT_FAILURE);
}
/* Allocates memory. */
Hsparse = UTILdoubleVector (nspin * maxnhtot);
Ssparse = UTILdoubleVector (maxnhtot);
numh = UTILintVector (no_u);
listh = UTILintVector (maxnhtot);
/* Reads the number of nonzero elements of each row of H. */
CHECKfread (fread (numh, no_u * sizeof (int), 1, gHS), 1, HSfile);
/* Reads the nonzero Hamiltonian-matrix */
/* element column indexes for each row. */
for (i = 0, k = 0; i < no_u; i++) {
CHECKfread (fread (&(listh[k]),
numh[i]*sizeof(int), 1, gHS), 1, HSfile);
k = k + numh[i];
}
/* Reads the Hamiltonian matrix in sparse form. */
for (j = 0, k = 0; j < nspin; j++)
for (i = 0; i < no_u; i++) {
CHECKfread (fread (&(Hsparse[k]),
numh[i]*sizeof(double), 1, gHS), 1, HSfile);
k = k + numh[i];
}
/* Reads the overlap matrix in sparse form. */
for (i = 0, k = 0; i < no_u; i++) {
CHECKfread (fread (&(Ssparse[k]),
numh[i]*sizeof (double), 1, gHS), 1, HSfile);
k = k + numh[i];
}
/* Assigns nonzero elements from 'Hsparse' and 'Ssparse'. */
/* The index 'k' runs over 'Hsparse' and 'Ssparse' matrices. */
for (i = 0, k = 0; i < no_u; i++)
for (j = 0; j < numh[i]; j++, k++) {
foo = (listh[k] - 1) % no_u; /* column index */
H[idx3d(i,foo,0,no_u,no_u)] += rydberg2eV * Hsparse[k];
S[idx(i,foo,no_u)] += Ssparse[k];
}
for (s = 1; s < nspin; s++) /* 'H' is bigger if 'nspin' > 1 */
for (i = 0, k = 0; i < no_u; i++)
for (j = 0; j < numh[i]; j++, k++) {
foo = (listh[k] - 1) % no_u; /* column index */
H[idx3d(i,foo,s,no_u,no_u)] += rydberg2eV * Hsparse[k];
}
/* "Shifts" the Fermi energy to 0. */
for (s = 0; s < nspin; s++)
for (i = 0; i < no_u; i++)
for (j = 0; j < no_u; j++)
H[idx3d(i,j,s,no_u,no_u)] -= ef[efIdx] * S[idx(i,j,no_u)];
/* Closes file. */
CHECKfclose (fclose (gHS), HSfile);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Frees memory. */
free (numh);
free (listh);
free (Hsparse);
free (Ssparse);
} /* readHSfile */
/* ********************************************************* */
/* Computes Hamiltonian derivative matrix by reading the */
/* Hamiltonian and overlap matrices from '.gHs' files for */
/* the displaced system. */
static void deltaH (double *dH, double *S0)
{
register int i, j, k, s, len;
double *Hm, *Hp, *S;
char *Hfile;
/* Allocates memory. */
Hm = UTILdoubleVector (3 * nDyn * nspin * no_u * no_u);
Hp = UTILdoubleVector (3 * nDyn * nspin * no_u * no_u);
S = CHECKmalloc (no_u * no_u * sizeof (double));
/* Sets the '.gHS' file name with 'FCdir' path. */
len = strlen (FCdir);
len += strlen (sysLabel);
Hfile = CHECKmalloc ((len + 9) * sizeof (char));
for (k = 0; k < 3 * nDyn; k++) {
/* 'H(-Q)' */
Hfile[0] = '\0';
sprintf (Hfile, "%s%s_%.3d.gHS", FCdir, sysLabel, 2 * k + 1);
UTILresetDoubleVector (no_u * no_u, S);
readHSfile (Hfile, &Hm[idx3d(0,0,k*nspin,no_u,no_u)], S, 2*k+1);
/* 'H(Q)' */
Hfile[0] = '\0';
sprintf (Hfile, "%s%s_%.3d.gHS", FCdir, sysLabel, 2 * k + 2);
UTILresetDoubleVector (no_u * no_u, S);
readHSfile (Hfile, &Hp[idx3d(0,0,k*nspin,no_u,no_u)], S, 2*k+2);
/* 'dH = {H(Q) - (ef(Q)-ef0)*S0 - [H(-Q)-(ef(-Q)-ef0)*S0]} / 2Q' */
/* or, simplifying: 'dH = {H(Q)-H(-Q)-[ef(Q)-ef(-Q)]*S0} / 2Q' */
for (s = 0; s < nspin; s++)
for (i = 0; i < no_u; i++)
for (j = 0; j < no_u; j++)
dH[idx3d(i,j,k*nspin+s,no_u,no_u)] =
(Hp[idx3d(i,j,k*nspin+s,no_u,no_u)]
- Hm[idx3d(i,j,k*nspin+s,no_u,no_u)]
- (ef[2*k+2] - ef[2*k+1]) * S0[idx(i,j,no_u)])
/ (2.0 * FCdispl);
}
/* Frees memory. */
free (Hfile);
free (Hp);
free (Hm);
free (S);
} /* deltaH */
/* ********************************************************* */
/* Reads the overlap matrix from '.onlyS' binary file. */
static void readOnlyS (char *Sfile, double *S)
{
register int i, j, k, foo;
int CKno_u, maxnhtot;
double *Ssparse, *Sbig;
int *numh, *listh;
FILE *OnlyS;
/* Opens the '.onlyS' binary file. */
printf (" reading \"%s\" file... ", Sfile);
OnlyS = CHECKfopen (Sfile, "rb");
/* Reads matrices dimensions and checks file consistency. */
fseek (OnlyS, 0L, SEEK_SET);
CHECKfread (fread (&CKno_u, sizeof (int), 1, OnlyS), 1, Sfile);
CHECKfread (fread (&maxnhtot, sizeof (int), 1, OnlyS), 1, Sfile);
if (CKno_u != 2 * no_u) {
fprintf (stderr,
" ERROR: the file %s is not written correctly!\n\n",
Sfile);
exit (EXIT_FAILURE);
}
/* Allocates memory. */
Ssparse = UTILdoubleVector (maxnhtot);
Sbig = UTILdoubleVector (2 * no_u * 2 * no_u);
numh = UTILintVector (2 * no_u);
listh = UTILintVector (maxnhtot);
/* Reads the number of nonzero elements of each row of S. */
CHECKfread (fread (numh, 2*no_u*sizeof(int), 1, OnlyS), 1, Sfile);
/* Reads the nonzero overlap-matrix */
/* element column indexes for each row. */
for (i = 0, k = 0; i < 2 * no_u; i++) {
CHECKfread (fread (&(listh[k]), numh[i]*sizeof(int),
1, OnlyS), 1, Sfile);
k = k + numh[i];
}
/* Reads the overlap matrix in sparse form. */
for (i = 0, k = 0; i < 2 * no_u; i++) {
CHECKfread (fread (&(Ssparse[k]), numh[i]*sizeof(double),
1, OnlyS), 1, Sfile);
k = k + numh[i];
}
/* Assigns nonzero elements from 'Ssparse'. */
/* The index 'k' runs over 'Ssparse' matrix. */
for (i = 0, k = 0; i < 2 * no_u; i++)
for (j = 0; j < numh[i]; j++, k++) {
foo = (listh[k] - 1) % (2 * no_u); /* column index */
Sbig[idx(i,foo,2*no_u)] += Ssparse[k];
}
/* Picks only the terms <i|j'> from dynamic atoms. */
for (j = 0; j < no_u; j++)
for (i = 0; i < no_u; i++)
S[idx(i,j,no_u)] = (Sbig[idx(i,j+no_u,2*no_u)]
+ Sbig[idx(j+no_u,i,2*no_u)]) / 2.0;
/* Closes file. */
CHECKfclose (fclose (OnlyS), Sfile);
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Frees memory. */
free (numh);
free (listh);
free (Ssparse);
free (Sbig);
} /* readOnlyS */
/* ********************************************************* */
/* Computes 'dS = [ <i|j(Q)> - <i|j(-Q)> ] / 2Q' by reading */
/* the overlap matrix from '.onlyS' files for the displaced */
/* system. */
static void deltaS (double *dS)
{
register int i, j, k, len;
double *Sm, *Sp;
char *Sfile;
/* Allocates memory and initializes with '0'. */
Sm = UTILdoubleVector (3 * no_u * no_u);
Sp = UTILdoubleVector (3 * no_u * no_u);
/* Sets the '.onlyS' file name with 'FCdir' path. */
len = strlen (FCdir);
len += strlen (sysLabel);
Sfile = CHECKmalloc ((len + 9) * sizeof (char));
for (k = 0; k < 3; k++) {
/* '<i|j(-Q)>' */
Sfile[0] = '\0';
sprintf (Sfile, "%s%s_%d.onlyS", FCdir, sysLabel, 2 * k + 1);
readOnlyS (Sfile, &Sm[idx3d(0,0,k,no_u,no_u)]);
/* '<i|j(Q)>' */
Sfile[0] = '\0';
sprintf (Sfile, "%s%s_%d.onlyS", FCdir, sysLabel, 2 * k + 2);
readOnlyS (Sfile, &Sp[idx3d(0,0,k,no_u,no_u)]);
/* 'dS = [ <i|j(Q)> - <i|j(-Q)> ] / 2Q' */
for (i = 0; i < no_u; i++)
for (j = 0; j < no_u; j++)
dS[idx3d(i,j,k,no_u,no_u)] =
(Sp[idx3d(i,j,k,no_u,no_u)] - Sm[idx3d(i,j,k,no_u,no_u)])
/ (2.0 * FCdispl);
}
/* Frees memory. */
free (Sfile);
free (Sp);
free (Sm);
} /* deltaS */
/* ********************************************************* */
/* Applies a correction due to the change in basis orbitals */
/* with displacement: */
/* 'dH = dH - dS*S0^-1*H0 - H0*S0^-1*(dS)^T' */
static void dHCorrection (double *dH, double *H0, double *S0)
{
register int i, j, k, s, coord, h;
int *ipiv;
double alpha, beta;
double *dStot, *dS, *invS0, *Aux;
/* Computes 'dS = [ <i|j(Q)> - <i|j(-Q)> ] / 2Q'. */
dStot = UTILdoubleVector (3 * no_u * no_u);
deltaS (dStot);
/* Initializes 'invS0' with 'S0'. */
invS0 = UTILdoubleVector (no_u * no_u);
UTILcopyVector (invS0, S0, no_u * no_u);
/* Computes 'invS0 = S0^-1'. */
ipiv = CHECKmalloc (no_u * sizeof (int));
CHECKdgetrf (no_u, invS0, ipiv); /* triangular matrix factorization */
CHECKdgetri (no_u, invS0, ipiv); /* matrix inversion */
/* Computes 'dH = dH - dS*S0^-1*H0 - H0*S0^-1*(dS)^T' */
/* for each displacement direction. */
printf ("\n correcting Hamiltonian derivatives elements... ");
dS = CHECKmalloc (no_u * no_u * sizeof (double));
Aux = CHECKmalloc (no_u * no_u * sizeof (double));
for (k = 0; k < nDyn; k++) {
UTILresetDoubleVector (no_u * no_u, dS);
for (coord = 0; coord < 3; coord++) { /* xyz */
/* The only non-zero elements from 'dS' matrix are those */
/* corresponding to the orbitals from the dynamic atom 'k'. */
for (j = orbIdx[FCfirst+k-1]; j < orbIdx[FCfirst+k]; j++)
for (i = 0; i < no_u; i++)
dS[idx(i,j,no_u)] = dStot[idx3d(i,j,coord,no_u,no_u)];
for (s = 0; s < nspin; s++) {
/* 'dH' index. */
h = (k * 3 + coord) * nspin+s;
/* 'Aux = - dS * S0^-1' */
alpha = - 1.0;
beta = 0.0; /* as 'beta = 0' -> no need to reset 'Aux' */
dgemm ("T","N", &no_u, &no_u, &no_u, &alpha, dS,
&no_u, invS0, &no_u, &beta, Aux, &no_u);
/* 'dH = dH + Aux * H0' */
alpha = beta = 1.0;
dgemm ("N","N", &no_u, &no_u, &no_u, &alpha, Aux, &no_u,
&H0[idx3d(0,0,s,no_u,no_u)], &no_u, &beta,
&dH[idx3d(0,0,h,no_u,no_u)], &no_u);
/* 'Aux = H0 * S0^-1' */
beta = 0.0;
dgemm ("N","N", &no_u, &no_u, &no_u, &alpha,
&H0[idx3d(0,0,s,no_u,no_u)], &no_u,
invS0, &no_u, &beta, Aux, &no_u);
/* 'dH = dH - Aux * (dS)^T' */
alpha = - 1.0;
beta = 1.0;
dgemm ("N","N", &no_u, &no_u, &no_u, &alpha, Aux, &no_u, dS,
&no_u, &beta, &dH[idx3d(0,0,h,no_u,no_u)], &no_u);
}
}
}
printf ("ok!\n");
setvbuf (stdout, NULL, _IONBF, 0); /* print now! */
/* Frees memory. */
free (ipiv);
free (dStot);
free (dS);
free (invS0);
free (Aux);
} /* dHCorrection */
/* ********************************************************* */
/* Having calculated the phonon energies ('EigVal') and */