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first commit, Readme.html更新して、git管理することにした。

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Takahiro OHKUBO
2023-05-26 20:13:05 +09:00
commit ce85e3907f
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read_lammpstrj.c
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#include "dump2analysis.h"
int GetHeader(FILE *fp, HEAD *head){
int chk;
char buf[1024];
double xlo = 0.0, xhi = 0.0, lx;
double ylo = 0.0, yhi = 0.0, ly;
double lz;
/* ITEM: TIMESTEP */
if (fgets(buf, sizeof(buf), fp)==NULL) return -1;
if (fgets(buf, sizeof(buf), fp)==NULL) return -1;
sscanf(buf, "%d", &head->step);
/* ITEM: NUMBER OF ATOMS */
fgets(buf, sizeof(buf), fp);
fgets(buf, sizeof(buf), fp);
sscanf(buf, "%d", &head->atoms);
/* ITEM: BOX BOUNDS xy xz yz pp pp pp */
fgets(buf, sizeof(buf), fp);
fgets(buf, sizeof(buf), fp);
chk = sscanf(buf, "%lf %lf %lf",&head->x_low, &head->x_hi, &head->xy);
if (chk == 2) {
head->A[0][0] = head->x_hi - head->x_low;
head->A[0][1] = 0.0;
head->A[0][2] = 0.0;
head->a = head->x_hi - head->x_low;
}
fgets(buf, sizeof(buf), fp);
chk = sscanf(buf, "%lf %lf %lf",&head->y_low, &head->y_hi, &head->xz);
if (chk == 2) {
head->A[1][0] = 0.0;
head->A[1][1] = head->y_hi - head->y_low ;
head->A[1][2] = 0.0;
head->b = head->y_hi - head->y_low;
}
fgets(buf, sizeof(buf), fp);
chk = sscanf(buf, "%lf %lf %lf", &head->z_low, &head->z_hi, &head->yz);
if (chk == 2) {
head->A[2][0] = 0.0;
head->A[2][1] = 0.0;
head->A[2][2] = head->z_hi - head->z_low ;
head->c = head->z_hi - head->z_low;
}
/* ITEM: ATOMS id element x y z vx vy vz fx fy fz */
fgets(buf, sizeof(buf), fp);
if (chk == 3){ /* triclinic */
/* x */
if (xlo > head->xy) xlo = head->xy;
if (xlo > head->xz) xlo = head->xz;
if (xlo > (head->xy+head->xz)) xlo = head->xy+head->xz;
if (xhi < head->xy) xhi = head->xy;
if (xhi < head->xz) xhi = head->xz;
if (xhi < (head->xy+head->xz)) xhi = head->xy+head->xz;
xlo = head->x_low - xlo;
xhi = head->x_hi - xhi;
lx = xhi - xlo;
head->a = lx;
/* y */
if (ylo > head->yz) ylo = head->yz;
if (yhi < head->yz) yhi = head->yz;
ylo = head->y_low - ylo;
yhi = head->y_hi - yhi;
ly = yhi - ylo;
head->b = sqrt(ly*ly + head->xy*head->xy);
/* z */
lz = head->z_hi - head->z_low;
head->c = sqrt(lz*lz + head->xz*head->xz + head->yz*head->yz );
/* angle */
head->alpha = acos((head->yz*ly+head->xy*head->xz)/
(head->b*head->c));
head->beta = acos(head->xz/head->c);
head->gamma = acos(head->xy/head->b);
head->A[0][0] = head->a;
head->A[0][1] = 0;
head->A[0][2] = 0;
head->A[1][0] = head->b*cos(head->gamma);
head->A[1][1] = head->b*sin(head->gamma);
head->A[1][2] = 0;
head->A[2][0] = head->c*cos(head->beta);
head->A[2][1] = head->c*(
cos(head->alpha)-cos(head->beta)*cos(head->gamma)
)/sin(head->gamma);
head->A[2][2] = head->c*sqrt(
1+2*cos(head->alpha)*cos(head->beta)*cos(head->gamma)
- cos(head->alpha)*cos(head->alpha)
- cos(head->beta)*cos(head->beta)
- cos(head->gamma)*cos(head->gamma)
) /sin(head->gamma);
}
else{ /* 直行系 */
head->alpha = M_PI*0.5;
head->beta = M_PI*0.5;
head->gamma = M_PI*0.5;
}
/* 逆行列の計算 */
double det_A;
det_A = head->A[0][0]*head->A[1][1]*head->A[2][2];
head->B[0][0] = (head->A[1][1]*head->A[2][2] - head->A[1][2]*head->A[2][1])/det_A;
head->B[1][0] = (head->A[1][2]*head->A[2][0] - head->A[1][0]*head->A[2][2])/det_A;
head->B[2][0] = (head->A[1][0]*head->A[2][1] - head->A[1][1]*head->A[2][0])/det_A;
head->B[0][1] = 0.0;
head->B[1][1] = (head->A[0][0]*head->A[2][2] - head->A[0][2]*head->A[2][0])/det_A;
head->B[2][1] = (head->A[0][1]*head->A[2][0] - head->A[0][0]*head->A[2][1])/det_A;
head->B[0][2] = 0.0;
head->B[1][2] = 0.0;
head->B[2][2] = (head->A[0][0]*head->A[1][1] - head->A[0][1]*head->A[1][0])/det_A;
return 1;
}
void SetData(HEAD *head, ATOMS *a, ATOMS *b){
double x, y, z;
x = b->x[0];
y = b->y[0];
z = b->z[0];
strcpy(a->elem[a->atoms], b->elem[0]);
a->id[a->atoms] = b->id[0];
a->type[a->atoms] = b->type[0];
/* 絶対座標を分率座標へ */
a->x[a->atoms] = x*head->B[0][0] + y*head->B[1][0] + z*head->B[2][0];
a->y[a->atoms] = x*head->B[0][1] + y*head->B[1][1] + z*head->B[2][1];
a->z[a->atoms] = x*head->B[0][2] + y*head->B[1][2] + z*head->B[2][2];
a->x[a->atoms] = a->x[a->atoms] - floor(a->x[a->atoms]);
a->y[a->atoms] = a->y[a->atoms] - floor(a->y[a->atoms]);
a->z[a->atoms] = a->z[a->atoms] - floor(a->z[a->atoms]);
a->vx[a->atoms] = b->vx[0];
a->vy[a->atoms] = b->vy[0];
a->vz[a->atoms] = b->vz[0];
a->fx[a->atoms] = b->fx[0];
a->fy[a->atoms] = b->fy[0];
a->fz[a->atoms] = b->fz[0];
a->atoms++;
}
void GetAllData(FILE *f, PARAM* p, HEAD *head, ATOMS *a){
int i;
char buf[1024];
ATOMS l;
Allocate(&l, 1);
GetHeader(f, head);
a->atoms = 0;
for(i=0; i<p->atoms; i++){
fgets(buf, sizeof(buf), f);
sscanf(buf, "%d %d %s %lf %lf %lf %lf %lf %lf %lf %lf %lf",
&l.id[0], &l.type[0], l.elem[0],
&l.x[0], &l.y[0], &l.z[0],
&l.vx[0], &l.vy[0], &l.vz[0],
&l.fx[0], &l.fy[0], &l.fz[0]
);
SetData(head, a, &l);
}
head->atoms = p->atoms;
}
void GetData(FILE *f, PARAM* p, HEAD *head, ATOMS *a, ATOMS *b, ATOMS *c){
int i, j;
char buf[1024];
ATOMS l;
Allocate(&l, 1);
if (a != NULL) a->atoms = 0;
if (b != NULL) b->atoms = 0;
if (c != NULL) c->atoms = 0;
GetHeader(f, head);
for(i=0; i<head->atoms; i++){
fgets(buf, sizeof(buf), f);
sscanf(buf, "%d %d %s %lf %lf %lf %lf %lf %lf %lf %lf %lf",
&l.id[0], &l.type[0], l.elem[0],
&l.x[0], &l.y[0], &l.z[0],
&l.vx[0], &l.vy[0], &l.vz[0],
&l.fx[0], &l.fy[0], &l.fz[0]
);
/* idで選択 */
for (j=1; j<p->Aid[0]; j++)
if (l.id[0] == p->Aid[j]) SetData(head, a, &l);
/* 元素名で選択 */
if (strcmp(p->Aelem, l.elem[0]) == 0) SetData(head, a, &l);
/* 元素タイプ番号で選択 */
if (p->Atype == l.type[0]) SetData(head, a, &l);
if (b == NULL) continue;
/* idで選択 */
for (j=1; j<p->Bid[0]; j++)
if (l.id[0] == p->Bid[j]) SetData(head, b, &l);
/* 元素名で選択 */
if (strcmp(p->Belem, l.elem[0]) == 0) SetData(head, b, &l);
/* 元素タイプ番号で選択 */
if (p->Btype == l.type[0]) SetData(head, b, &l);
if (c == NULL) continue;
/* idで選択 */
for (j=1; j<p->Cid[0]; j++)
if (l.id[0] == p->Cid[j]) SetData(head, c, &l);
/* 元素名で選択 */
if (strcmp(p->Celem, l.elem[0]) == 0) SetData(head, c, &l);
/* 元素タイプ番号で選択 */
if (p->Ctype == l.type[0]) SetData(head, c, &l);
}
}
void GetOneStepData(FILE *f, HEAD *head, ATOMS *a){
int i;
double x, y, z;
char buf[1024];
GetHeader(f, head);
for(i=0; i<head->atoms; i++){
fgets(buf, sizeof(buf), f);
sscanf(buf, "%d %d %s %lf %lf %lf %lf %lf %lf %lf %lf %lf",
&a->id[i], &a->type[i], a->elem[i],
&x, &y, &z,
&a->vx[i], &a->vy[i], &a->vz[i],
&a->fx[i], &a->fy[i], &a->fz[i]);
/* 絶対座標を分率座標へ 2017-12-27に修正 */
a->x[i] = x*head->B[0][0] + y*head->B[1][0] + z*head->B[2][0];
a->y[i] = x*head->B[0][1] + y*head->B[1][1] + z*head->B[2][1];
a->z[i] = x*head->B[0][2] + y*head->B[1][2] + z*head->B[2][2];
a->x[i] = a->x[i] - floor(a->x[i]);
a->y[i] = a->y[i] - floor(a->y[i]);
a->z[i] = a->z[i] - floor(a->z[i]);
}
}
void SetIDfromElemTtype(PARAM *param){
int i, j;
ATOMS a;
FILE *f;
HEAD head;
/* 構造体のメモリ確保 */
Allocate(&a, param->atoms);
/* ファイルオープン */
f = fopen(param->infile, "r");
GetOneStepData(f, &head, &a);
/* 元素名で指定した場合はidに変換 */
if (strcmp(param->Aelem, "") != 0){
j = 0;
for (i=0; i<a.atoms; i++){
if (strcmp(a.elem[i], param->Aelem) == 0){
param->Aid = realloc(param->Aid, sizeof(int) * (j + 2));
param->Aid[j+1] = a.id[i];
j++;
}
}
param->Atype = -1;
strcpy(param->Aelem, "");
param->Aid[0] = j+1;
}
/* 元素タイプで指定した場合はidに変換 */
if (param->Atype != -1){
j = 0;
for (i=0; i<a.atoms; i++){
if (param->Atype == a.type[i]){
param->Aid = realloc(param->Aid, sizeof(int) * (j + 2));
param->Aid[j+1] = a.id[i];
j++;
}
}
param->Atype = -1;
strcpy(param->Aelem, "");
param->Aid[0] = j+1;
}
fclose(f);
}
int* SetIDfromMolecules(int *Aid, int n){
int i, j;
int *tmp;
int atoms;
/* 指定原子から連番で原子の数(n)だけ選択原子を増やす */
atoms = (Aid[0]-1) * n;
tmp = malloc(sizeof(int) * atoms + 1);
tmp[0] = atoms + 1;
for (i=1; i<Aid[0]; i++){
tmp[(i-1)*n + 1] = Aid[i];
for (j=0; j<n; j++){
tmp[(i-1)*n + 1 + j + 1] = Aid[i] + j + 1;
}
}
Aid = malloc(sizeof(int)*tmp[0]);
Aid[0] = tmp[0];
for (i=1; i<Aid[0]; i++)
Aid[i] = tmp[i];
return Aid;
}
void Unwrap(int steps, int atoms, double **x, double **y, double **z){
int **nx, **ny, **nz;
int i, j;
nx = malloc(sizeof(int*) * steps);
ny = malloc(sizeof(int*) * steps);
nz = malloc(sizeof(int*) * steps);
for (i=0; i < steps; i++){
nx[i] = malloc(sizeof(int) * atoms);
ny[i] = malloc(sizeof(int) * atoms);
nz[i] = malloc(sizeof(int) * atoms);
}
for (i=0; i<steps; i++){
for (j=0; j<atoms; j++){
nx[i][j] = 0;
ny[i][j] = 0;
nz[i][j] = 0;
}
}
for (i=1; i<steps; i++){
for (j=0; j<atoms; j++){
nx[i][j] = nx[i-1][j] + round(x[i-1][j] - x[i][j]);
ny[i][j] = ny[i-1][j] + round(y[i-1][j] - y[i][j]);
nz[i][j] = nz[i-1][j] + round(z[i-1][j] - z[i][j]);
}
}
for (i=0; i<steps; i++){
for (j=0; j<atoms; j++){
x[i][j] = x[i][j] + (double)nx[i][j];
y[i][j] = y[i][j] + (double)ny[i][j];
z[i][j] = z[i][j] + (double)nz[i][j];
}
}
}