return_type2
generate2()
{
return_type2 r(generate_vec(), x());
if (disable_rvo)
return r;
return return_type2();
}
return_type
generate()
{
return_type r(generate_vec());
if (disable_rvo)
return r;
return return_type();
}
double minimize_md()
{
static int ct_AN,num1,num2,po,num_trial;
static int ix,iy,iz,iq1,iq2,iq3;
static double sumx,sumy,sumz;
static double cx1,cy1,cz1;
static double cx2,cy2,cz2;
static double **xyz2;
static double MaxX,MaxY,MaxZ,MaxQ1,MaxQ2,MaxQ3;
static double MinX,MinY,MinZ,MinQ1,MinQ2,MinQ3;
static double dX,dY,dZ,dQ1,dQ2,dQ3;
static double Min_MD,Last_Min_MD;
static double Sx,Sy,Sz,Cx,Cy,Cz;
static double Q1,Q2,Q3,x,y,z,dum;
static double Fx,Fy,Fz,FQ1,FQ2,FQ3;
static double Rot[5][5];
/* allocation of array */
xyz2 = (double**)malloc(sizeof(double*)*(atomnum2+1));
for (ct_AN=0; ct_AN<=atomnum2; ct_AN++){
xyz2[ct_AN] = (double*)malloc(sizeof(double)*4);
}
/* find the centroid */
sumx = 0.0;
sumy = 0.0;
sumz = 0.0;
for (ct_AN=1; ct_AN<=atomnum1; ct_AN++){
sumx += Gxyz1[ct_AN][1];
sumy += Gxyz1[ct_AN][2];
sumz += Gxyz1[ct_AN][3];
}
cx1 = cx1/(double)atomnum1;
cy1 = cy1/(double)atomnum1;
cz1 = cz1/(double)atomnum1;
sumx = 0.0;
sumy = 0.0;
sumz = 0.0;
for (ct_AN=1; ct_AN<=atomnum2; ct_AN++){
sumx += Gxyz2[ct_AN][1];
sumy += Gxyz2[ct_AN][2];
sumz += Gxyz2[ct_AN][3];
}
cx2 = cx2/(double)atomnum2;
cy2 = cy2/(double)atomnum2;
cz2 = cz2/(double)atomnum2;
/* shift the centroid to the origin */
for (ct_AN=1; ct_AN<=atomnum1; ct_AN++){
Gxyz1[ct_AN][1] -= cx1;
Gxyz1[ct_AN][2] -= cy1;
Gxyz1[ct_AN][3] -= cz1;
}
for (ct_AN=1; ct_AN<=atomnum2; ct_AN++){
Gxyz2[ct_AN][1] -= cx2;
Gxyz2[ct_AN][2] -= cy2;
Gxyz2[ct_AN][3] -= cz2;
}
po = 0;
num1 = 12;
num2 = 20;
num_trial = 1;
Last_Min_MD = 10000.0;
Min_MD = 1.0e+10;
do {
if (num_trial==1){
MaxX = 0.05;
MinX = -0.05;
MaxY = 0.05;
MinY = -0.05;
MaxZ = 0.05;
MinZ = -0.05;
MaxQ1 = 0.2;
MinQ1 = 0.0;
MaxQ2 = 0.2;
MinQ2 = 0.0;
MaxQ3 = 0.2;
MinQ3 = 0.0;
}
else {
MaxX = Fx + 2.0*dX;
MinX = Fx - 2.0*dX;
MaxY = Fy + 2.0*dY;
MinY = Fy - 2.0*dY;
MaxZ = Fz + 2.0*dZ;
MinZ = Fz - 2.0*dZ;
MaxQ1 = FQ1 + 2.0*dQ1;
MinQ1 = FQ1 - 2.0*dQ1;
MaxQ2 = FQ2 + 2.0*dQ2;
MinQ2 = FQ2 - 2.0*dQ2;
MaxQ3 = FQ3 + 2.0*dQ3;
MinQ3 = FQ3 - 2.0*dQ3;
}
dX = (MaxX - MinX)/(double)num1;
dY = (MaxY - MinY)/(double)num1;
dZ = (MaxZ - MinZ)/(double)num1;
dQ1 = (MaxQ1 - MinQ1)/(double)num2;
dQ2 = (MaxQ2 - MinQ2)/(double)num2;
dQ3 = (MaxQ3 - MinQ3)/(double)num2;
for (ix=0; ix<num1; ix++){
x = MinX + ix*dX;
for (iy=0; iy<num1; iy++){
y = MinY + iy*dY;
for (iz=0; iz<num1; iz++){
z = MinZ + iz*dZ;
for (iq1=0; iq1<num2; iq1++){
Q1 = MinQ1 + iq1*dQ1;
Sx = sin(Q1);
Cx = cos(Q1);
for (iq2=0; iq2<num2; iq2++){
Q2 = MinQ2 + iq2*dQ2;
Sy = sin(Q2);
Cy = cos(Q2);
for (iq3=0; iq3<num2; iq3++){
Q3 = MinQ3 + iq3*dQ3;
Sz = sin(Q3);
Cz = cos(Q3);
/* make a transform matrix */
Rot[1][1] = Cy*Cz;
Rot[1][2] = Sx*Sy*Cz - Cx*Sz;
Rot[1][3] = Cx*Sy*Cz + Sx*Sz;
Rot[2][1] = Cy*Sz;
Rot[2][2] = Sx*Sy*Sz + Cx*Cz;
Rot[2][3] = Cx*Sy*Sz - Sx*Cz;
Rot[3][1] = -Sy;
Rot[3][2] = Sx*Cy;
Rot[3][3] = Cx*Cy;
for (ct_AN=1; ct_AN<=atomnum1; ct_AN++){
xyz2[ct_AN][1] = Rot[1][1]*(Gxyz2[ct_AN][1]-x)
+ Rot[1][2]*(Gxyz2[ct_AN][2]-y)
+ Rot[1][3]*(Gxyz2[ct_AN][3]-z);
xyz2[ct_AN][2] = Rot[2][1]*(Gxyz2[ct_AN][1]-x)
+ Rot[2][2]*(Gxyz2[ct_AN][2]-y)
+ Rot[2][3]*(Gxyz2[ct_AN][3]-z);
xyz2[ct_AN][3] = Rot[3][1]*(Gxyz2[ct_AN][1]-x)
+ Rot[3][2]*(Gxyz2[ct_AN][2]-y)
+ Rot[3][3]*(Gxyz2[ct_AN][3]-z);
}
dum = md(Gxyz1, xyz2);
if (dum<Min_MD){
Min_MD = dum;
Fx = x;
Fy = y;
Fz = z;
FQ1 = Q1;
FQ2 = Q2;
FQ3 = Q3;
printf(" trial=%2d x,y,z=%6.3f %6.3f %6.3f Q1,Q2,Q3=%6.3f %6.3f %6.3f MD=%12.9f\n",
num_trial,x,y,z,Q1/PI*180.0,Q2/PI*180.0,Q3/PI*180.0,dum);
}
}
}
}
}
}
}
if ( fabs(Last_Min_MD-Min_MD)<1.0e-5 ) po = 1;
printf(" MD (previous trial)=%15.12f MD (current trial)=%15.12f\n",
Last_Min_MD,Min_MD);
Last_Min_MD = Min_MD;
num_trial++;
} while (po==0);
printf("\n");
printf(" Final MD (Ang/N)=%15.12f\n",Min_MD);
printf(" Translated x,y,z (Ang) of centroid = %6.3f %6.3f %6.3f\n",Fx,Fy,Fz);
printf(" Rotation Angles Q1,Q2,Q3 (Deg) = %6.3f %6.3f %6.3f\n",
FQ1/PI*180.0,FQ2/PI*180.0,FQ3/PI*180.0);
/* generate a vector file */
Sx = sin(FQ1);
Cx = cos(FQ1);
Sy = sin(FQ2);
Cy = cos(FQ2);
Sz = sin(FQ3);
Cz = cos(FQ3);
Rot[1][1] = Cy*Cz;
Rot[1][2] = Sx*Sy*Cz - Cx*Sz;
Rot[1][3] = Cx*Sy*Cz + Sx*Sz;
Rot[2][1] = Cy*Sz;
Rot[2][2] = Sx*Sy*Sz + Cx*Cz;
Rot[2][3] = Cx*Sy*Sz - Sx*Cz;
Rot[3][1] = -Sy;
Rot[3][2] = Sx*Cy;
Rot[3][3] = Cx*Cy;
for (ct_AN=1; ct_AN<=atomnum1; ct_AN++){
xyz2[ct_AN][1] = Rot[1][1]*(Gxyz2[ct_AN][1]-Fx)
+ Rot[1][2]*(Gxyz2[ct_AN][2]-Fy)
+ Rot[1][3]*(Gxyz2[ct_AN][3]-Fz);
xyz2[ct_AN][2] = Rot[2][1]*(Gxyz2[ct_AN][1]-Fx)
+ Rot[2][2]*(Gxyz2[ct_AN][2]-Fy)
+ Rot[2][3]*(Gxyz2[ct_AN][3]-Fz);
xyz2[ct_AN][3] = Rot[3][1]*(Gxyz2[ct_AN][1]-Fx)
+ Rot[3][2]*(Gxyz2[ct_AN][2]-Fy)
+ Rot[3][3]*(Gxyz2[ct_AN][3]-Fz);
}
printf(" generate a vector file, dgeo_vec.txt\n\n");
generate_vec(Gxyz1, xyz2);
/* freeing of array */
for (ct_AN=0; ct_AN<=atomnum2; ct_AN++){
free(xyz2[ct_AN]);
}
free(xyz2);
}
int main(int argc, char *argv[])
{
static int i,po_d,d_i,anal_switch;
static char file1[100];
static char file2[100];
printf("\n******************************************************************\n");
printf("******************************************************************\n");
printf(" diff_geo: analysis of structural deviation.\n");
printf(" Copyright (C), 2004, Taisuke Ozaki \n");
printf(" This is free software, and you are welcome to \n");
printf(" redistribute it under the constitution of the GNU-GPL.\n");
printf("******************************************************************\n");
printf("******************************************************************\n\n");
if (argc!=5 && argc!=6){
printf("Usage:\n");
printf(" ./diff_geo file1.xyz file2.xyz -d rmsd\n\n");
printf(" option\n");
printf(" -d rmsd a root mean square of deviation\n");
printf(" -d md a mean deviation\n");
printf(" -d mdbl 2.2 a mean deviation between bond lengths\n");
printf(" 2.2 (Ang) means a cutoff bond length which\n");
printf(" can be taken into account in the calculation\n\n");
exit(0);
}
po_d = 0;
for (i=1; i<argc; i++){
if (strcmp(argv[i],"-d")==0){
po_d = 1;
d_i = i;
}
}
if (strcmp(argv[d_i+1],"rmsd")==0){
anal_switch = 1;
if (argc!=5){
printf("Usage:\n");
printf(" ./diff_geo file1.xyz file2.xyz -d rmsd\n\n");
printf(" option\n");
printf(" -d rmsd a root mean square of deviation\n");
printf(" -d md a mean deviation\n");
printf(" -d mdbl a mean deviation between bond lengths\n\n");
printf(" 2.2 (Ang) means a cutoff bond length which\n");
printf(" can be taken into account in the calculation\n\n");
exit(0);
}
}
else if (strcmp(argv[d_i+1],"md")==0){
anal_switch = 2;
if (argc!=5){
printf("Usage:\n");
printf(" ./diff_geo file1.xyz file2.xyz -d md\n\n");
printf(" option\n");
printf(" -d rmsd a root mean square of deviation\n");
printf(" -d md a mean deviation\n");
printf(" -d mdbl a mean deviation between bond lengths\n\n");
printf(" 2.2 (Ang) means a cutoff bond length which\n");
printf(" can be taken into account in the calculation\n\n");
exit(0);
}
}
else if (strcmp(argv[d_i+1],"mdbl")==0){
anal_switch = 3;
if (argc!=6){
printf("Usage:\n");
printf(" ./diff_geo file1.xyz file2.xyz -d mdbl 2.2\n\n");
printf(" option\n");
printf(" -d rmsd a root mean square of deviation\n");
printf(" -d md a mean deviation\n");
printf(" -d mdbl a mean deviation between bond lengths\n\n");
printf(" 2.2 (Ang) means a cutoff bond length which\n");
printf(" can be taken into account in the calculation\n\n");
exit(0);
}
BL0 = atof(argv[d_i+2]);
if (BL0<0.0){
printf("Cutoff bond length is negative.\n");
exit(0);
}
}
else{
printf(" This option is not supported.\n");
exit(0);
}
sprintf(file1,"%s",argv[1]);
sprintf(file2,"%s",argv[2]);
read_xyzfiles(file1, file2);
/* a root mean square of deviation */
if (anal_switch==1){
minimize_rmsd();
}
/* a mean deviation */
else if (anal_switch==2){
minimize_md();
}
/* a mean deviation between bond lengths */
else if (anal_switch==3){
calc_md_BL();
}
/* generate a vector file */
else if (anal_switch==4){
generate_vec();
}
}
