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
|
/************************************************
set density_grid on the electrode
interpolate Density_Grid_e
and setup Density_Grid on the electrodes ( mesh points are different )
***************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#ifdef nompi
#include "mimic_mpi.h"
#else
#include "mpi.h"
#endif
#include "tran_prototypes.h"
#define print_stdout 0
double Dot_Product(double a[4], double b[4]);
void Cross_Product(double a[4], double b[4], double c[4]);
#define PI 3.1415926535897932384626
static void Convert_Cell_tv(double tv[4][4], double pos[4],
/* output*/ double xyz[4])
{
double a[4];
double rtv[4][4];
double tmpv[4], CellV;
Cross_Product(tv[2],tv[3],tmpv);
CellV = Dot_Product(tv[1],tmpv);
Cross_Product(tv[2],tv[3],tmpv);
rtv[1][1] = 2.0*PI*tmpv[1]/CellV;
rtv[1][2] = 2.0*PI*tmpv[2]/CellV;
rtv[1][3] = 2.0*PI*tmpv[3]/CellV;
Cross_Product(tv[3],tv[1],tmpv);
rtv[2][1] = 2.0*PI*tmpv[1]/CellV;
rtv[2][2] = 2.0*PI*tmpv[2]/CellV;
rtv[2][3] = 2.0*PI*tmpv[3]/CellV;
Cross_Product(tv[1],tv[2],tmpv);
rtv[3][1] = 2.0*PI*tmpv[1]/CellV;
rtv[3][2] = 2.0*PI*tmpv[2]/CellV;
rtv[3][3] = 2.0*PI*tmpv[3]/CellV;
if (print_stdout){
printf("Convert_Cell_tv, pos= %lf %lf %lf ", pos[1], pos[2], pos[3]);
}
a[1] = Dot_Product(pos,rtv[1])*0.5/PI;
a[2] = Dot_Product(pos,rtv[2])*0.5/PI;
a[3] = Dot_Product(pos,rtv[3])*0.5/PI;
if (print_stdout){
printf("x= %lf %lf %lf ", a[1], a[2], a[3]);
}
a[1] *= sqrt(Dot_Product(tv[1],tv[1]));
a[2] *= sqrt(Dot_Product(tv[2],tv[2]));
a[3] *= sqrt(Dot_Product(tv[3],tv[3]));
xyz[1]= a[1];
xyz[2]= a[2];
xyz[3]= a[3];
if (print_stdout){
printf("x*|tv|= %lf %lf %lf\n", xyz[1], xyz[2], xyz[3]);
}
}
/**************************************************
N_e = Ngrid1_e* Ngrid2_e* Ngrid3_e
Density_Grid_e[][N_e]
mesh point is tv_e[4][4]
N = Ngrid1* Ngrid2* Ngrid3
Density_Grid[][N]
mesh point is tv[4][4]
purpose:
interpolate Density_Grid_e to fit the mesh points of Density_Grid
This subroutine is to be used also so as to interpolate data of Vpot_Grid.
note:
Density_Grid_ref(i,j,k) = Density_Grid[MN]
MN = i*Ngrid2*Ngrid3 + j*Ngrid3 + k;
i=0...Ngrid1-1
j=
k=
**************************************************/
void TRAN_Interp_ElectrodeDensity_Grid(
MPI_Comm comm1,
double offset[4], /* input. use offset[1..3], = dx */
/* left edge is gtv*offset */
double *Density_Grid_e , /* input */
int Ngrid1_e, int Ngrid2_e, int Ngrid3_e, /* input */
double tv_e[4][4], /* input, unit cell vector of electrode, from inputfile not from saved data */
double gtv_e[4][4], /* input, cell vector of electrode */
double *Density_Grid, /* <=== output */
int Ngrid1, int Ngrid2, int Ngrid3,
int l1boundary[2], /* input */
double tv[4][4], /* input, unit cell vector */
double gtv[4][4] /* input, cell vector */
)
{
int i,j,k;
int id;
int po; /* error flag */
int n_in[3], n_out[4];
double angle,sign,factor;
double alpha[3],beta[3],gamma[3];
double grids[4],grids_e[4];
double Xgtv_e[4], Xgtv[4], Xtv_e[4], Xoffset[4];
/* mesh on the electrode is gtv_e*(1/2+integer) */
/* mesh on the CLR system is gtv*(1/2+integer) */
/* first check tv[1] and tv[2] have the same direction as tv_e[1] and tv_e[2] */
po=0; /* error flag */
for (id=2;id<=3;id++) {
for (i=1;i<=3;i++) {
if ( 1.0e-20<fabs(tv_e[id][i]-tv[id][i]) ) po++;
}
}
if (po) {
/* tv and tv_electrode is different */
printf("a and/or b axis of tv and tv_electrode is different\n");
exit(0);
}
/* check whether the direction of tv[1] and tv_e[1] is 0 or pi */
angle = Dot_Product( tv[1], tv_e[1]);
if (angle<0) {
printf("c direction of this system is different from that of the electrode\n");
exit(0);
}
/***************************************************************************
* positions
* electrode mesh LCR mesh
* (1/2+i_e)*gtv_e => dx + (1/2+i0+i)*gtv, integer: i_e,i,i0
* i_e = [0:Ngrid_e-1] i=[0:N1-1]
*
* (1/2+i_e)*tv_e/Ngrid_e
*
* [(1/2+i_e)/Ngrid_e] *tv_e
* dx + (1/2+i0+i)*gtv
* = (dx + (1/2+i0+i)*gtv )/tv_e * tv_e
* = (dx/tv_e + (1/2+i0+i)*gtv/tv_e) * tv_e
* = (dx/tv_e + (1/2+i0+i)*gtv/gtv_e/Ngrid) *tv_e
* = {(dx/tv_e + (1/2+i0+i)*gtv/gtv_e/Ngrid)*N1 /N1 } *tv_e
*
*
*
* 0<[(1/2+i_e)/Ngrid_e]<1
* alpha = dx/tv_e*Ngrid + (1/2+i0)*tv/tv_e, beta = tv/tv_e
*
*
***************************************************************************/
for (i=1;i<=3;i++) {
gamma[i-1]=0.5;
}
grids_e[1]=Ngrid1_e;
grids_e[2]=Ngrid2_e;
grids_e[3]=Ngrid3_e;
grids[1] = l1boundary[1]-l1boundary[0]+1;
grids[2] = Ngrid2;
grids[3] = Ngrid3;
#if 1
Convert_Cell_tv(tv,offset,Xoffset);
for (i=1;i<=3;i++) {
Xgtv[i]= sqrt(Dot_Product(gtv[i],gtv[i]));
Xtv_e[i] = sqrt(Dot_Product(tv_e[i],tv_e[i]));
Xgtv_e[i] = sqrt(Dot_Product(gtv_e[i],gtv_e[i]));
}
for (i=1;i<=3;i++) {
factor = Xgtv[i]/Xgtv_e[i]/(double)grids_e[i]*(double)grids[i];
if (i==1) {
alpha[i-1]=Xoffset[i]/Xtv_e[i]*grids[i]+ (0.5+l1boundary[0])*factor;
}
else {
alpha[i-1]=Xoffset[i]/Xtv_e[i]*grids[i]+ (0.5)*factor;
}
/* start from l3boundary[0] */
beta[i-1] = factor;
}
#else
for (i=1;i<=3;i++) {
factor = sqrt(Dot_Product(gtv[i],gtv[i]))/sqrt(Dot_Product(gtv_e[i],gtv_e[i]))/grids_e[i]*grids[i];
alpha[i-1]=offset[i]/sqrt(Dot_Product(tv_e[i],tv_e[i]))*grids[i]+(0.5+l3boundary[0])*factor;
/* start from l3boundary[0] */
beta[i-1] = factor;
}
#endif
/* debug */
/* alpha[2]=0.5*(l3boundary[1]-l3boundary[0]+1)/Ngrid3_e;
* beta[2]=1.0*(l3boundary[1]-l3boundary[0]+1)/Ngrid3_e;
*/
if (print_stdout){
for (i=0;i<3;i++) {
printf("alpha,beta,gamma=%lf %lf %lf\n",alpha[i],beta[i],gamma[i]);
}
}
/* interpolate it */
/* interpolation */
n_in[0]=Ngrid1_e;
n_in[1]=Ngrid2_e;
n_in[2]=Ngrid3_e;
n_out[0]=l1boundary[1]-l1boundary[0]+1;
n_out[1]=Ngrid2;
n_out[2]=Ngrid3;
n_out[3]=l1boundary[1]-l1boundary[0];
if (print_stdout){
printf("nin = %d %d %d\n", n_in[0], n_in[1], n_in[2]);
printf("nout = %d %d %d %d\n", n_out[0], n_out[1], n_out[2],n_out[3]);
}
TRAN_FFT_Dinterpolation3D(comm1, n_in, Density_Grid_e, n_out, Density_Grid,
alpha,beta,gamma);
}
|
