void Boresight_transformation::fill_params_outer_bore()
{ //todo change Rotation
//cam koordinate system
//Translation
m_translation_cam = m_cam.get_O();
//Rotation
m_rotation_cam = Rotation_matrix(Rotation_matrix::math,m_cam.get_rotX(),m_cam.get_rotY(),m_cam.get_rotZ());
//car koordinate system
//Translation
m_translation_car = m_cam.get_B();
//Rotation
m_rotation_car = Rotation_matrix(Rotation_matrix::math,m_cam.get_B_rotx(),m_cam.get_B_roty(),m_cam.get_B_rotz());
}
void Boresight_transformation::fill_params_global()
{//todo change Rotation
//gps coordinate system
//Translation
m_translation_global = Point(m_Easting,m_Northing,m_ell_Height,m_dEasting,m_dNorthing,m_dell_Height);
//Rotation
//m_rotation_global = Rot(m_pitch,m_roll,m_heading);
m_rotation_global = Rotation_matrix(Rotation_matrix::math,m_roll,m_pitch,m_heading);
//std::cout<<std::endl<<"Rnach: "<<m_rotation_global<<std::flush;
}
void read_xtc2structure(char * filename,char * out_file, int ion_position,vector<int> quartet_1_serial,vector<int> quartet_2_serial,struct atom * atom_head,int step_frame )
{
int natoms,step;
float time_temp;
float p;
matrix box;
rvec *x;
XDRFILE *xtc;
xtc=xdrfile_open(filename,"r");
int read_return=read_xtc_natoms(filename,&natoms);
int num_step=0;
ofstream out(out_file);
out<<"#calculate the distence of ion to the center of the two quartets in z-axis/"<<endl;
out<<"#Time\t"<<"dist2ions"<<"\t"<<"dist2quartets"<<endl;
double * ion_coor;
ion_coor=dvector(0,2);
struct chain * chain_head;
chain_head=read_pdb_to_chain(atom_head);
struct chain * ch_q_1_G_1;
struct chain * ch_q_1_G_2;
struct chain * ch_q_1_G_3;
struct chain * ch_q_1_G_4;
struct chain * ch_q_2_G_1;
struct chain * ch_q_2_G_2;
struct chain * ch_q_2_G_3;
struct chain * ch_q_2_G_4;
ch_q_1_G_1=get_base_chain(chain_head,quartet_1_serial.at(0));
ch_q_1_G_2=get_base_chain(chain_head,quartet_1_serial.at(1));
ch_q_1_G_3=get_base_chain(chain_head,quartet_1_serial.at(2));
ch_q_1_G_4=get_base_chain(chain_head,quartet_1_serial.at(3));
ch_q_2_G_1=get_base_chain(chain_head,quartet_2_serial.at(0));
ch_q_2_G_2=get_base_chain(chain_head,quartet_2_serial.at(1));
ch_q_2_G_3=get_base_chain(chain_head,quartet_2_serial.at(2));
ch_q_2_G_4=get_base_chain(chain_head,quartet_2_serial.at(3));
struct base_purine_serial * bs_q_1_G_1;
struct base_purine_serial * bs_q_1_G_2;
struct base_purine_serial * bs_q_1_G_3;
struct base_purine_serial * bs_q_1_G_4;
struct base_purine_serial * bs_q_2_G_1;
struct base_purine_serial * bs_q_2_G_2;
struct base_purine_serial * bs_q_2_G_3;
struct base_purine_serial * bs_q_2_G_4;
//得到G碱基的原子的序号。
bs_q_1_G_1=read_pdb2purine_base(atom_head,*ch_q_1_G_1);
bs_q_1_G_2=read_pdb2purine_base(atom_head,*ch_q_1_G_2);
bs_q_1_G_3=read_pdb2purine_base(atom_head,*ch_q_1_G_3);
bs_q_1_G_4=read_pdb2purine_base(atom_head,*ch_q_1_G_4);
bs_q_2_G_1=read_pdb2purine_base(atom_head,*ch_q_2_G_1);
bs_q_2_G_2=read_pdb2purine_base(atom_head,*ch_q_2_G_2);
bs_q_2_G_3=read_pdb2purine_base(atom_head,*ch_q_2_G_3);
bs_q_2_G_4=read_pdb2purine_base(atom_head,*ch_q_2_G_4);
x=(rvec * )calloc(natoms,sizeof(x[0]));
while(1)
{
read_return=read_xtc(xtc,natoms,&step,&time_temp,box,x,&p);
num_step++;
if(step%10000==0)
{
cout<<"Reading frame : "<<step<<"\t time :"<<time_temp<<endl;
}
if(read_return!=0)
{
break;
}
if(num_step%step_frame==0)
{
double ** q_1_G_1_matrix;
double ** q_1_G_2_matrix;
double ** q_1_G_3_matrix;
double ** q_1_G_4_matrix;
double ** q_2_G_1_matrix;
double ** q_2_G_2_matrix;
double ** q_2_G_3_matrix;
double ** q_2_G_4_matrix;
q_1_G_1_matrix=dmatrix(0,8,0,2);
q_1_G_2_matrix=dmatrix(0,8,0,2);
q_1_G_3_matrix=dmatrix(0,8,0,2);
q_1_G_4_matrix=dmatrix(0,8,0,2);
q_2_G_1_matrix=dmatrix(0,8,0,2);
q_2_G_2_matrix=dmatrix(0,8,0,2);
q_2_G_3_matrix=dmatrix(0,8,0,2);
q_2_G_4_matrix=dmatrix(0,8,0,2);
for(int i=0;i<natoms;i++)
{
// cout<<step<<"\t"<<time_temp<<"\t"<<natom<<"\t"<<x[natom][0]<<"\t"<<x[natom][1]<<"\t"<<x[natom][2]<<endl;
if((i+1)==ion_position)
{
ion_coor[0]=10*x[i][0];
ion_coor[1]=10*x[i][1];
ion_coor[2]=10*x[i][2];
// cout<<"get ions coordination"<<endl;
}
//q_1_G_1
if((i+1)==bs_q_1_G_1->C2_serial)
{
q_1_G_1_matrix[6][0]=10*x[i][0];
q_1_G_1_matrix[6][1]=10*x[i][1];
q_1_G_1_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->C4_serial)
{
q_1_G_1_matrix[8][0]=10*x[i][0];
q_1_G_1_matrix[8][1]=10*x[i][1];
q_1_G_1_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->C5_serial)
{
q_1_G_1_matrix[3][0]=10*x[i][0];
q_1_G_1_matrix[3][1]=10*x[i][1];
q_1_G_1_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->C6_serial)
{
q_1_G_1_matrix[4][0]=10*x[i][0];
q_1_G_1_matrix[4][1]=10*x[i][1];
q_1_G_1_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->C8_serial)
{
q_1_G_1_matrix[1][0]=10*x[i][0];
q_1_G_1_matrix[1][1]=10*x[i][1];
q_1_G_1_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->N1_serial)
{
q_1_G_1_matrix[5][0]=10*x[i][0];
q_1_G_1_matrix[5][1]=10*x[i][1];
q_1_G_1_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->N3_serial)
{
q_1_G_1_matrix[7][0]=10*x[i][0];
q_1_G_1_matrix[7][1]=10*x[i][1];
q_1_G_1_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->N7_serial)
{
q_1_G_1_matrix[2][0]=10*x[i][0];
q_1_G_1_matrix[2][1]=10*x[i][1];
q_1_G_1_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_1->N9_serial)
{
q_1_G_1_matrix[0][0]=10*x[i][0];
q_1_G_1_matrix[0][1]=10*x[i][1];
q_1_G_1_matrix[0][2]=10*x[i][2];
}
// q_1_G_2
if((i+1)==bs_q_1_G_2->C2_serial)
{
q_1_G_2_matrix[6][0]=10*x[i][0];
q_1_G_2_matrix[6][1]=10*x[i][1];
q_1_G_2_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->C4_serial)
{
q_1_G_2_matrix[8][0]=10*x[i][0];
q_1_G_2_matrix[8][1]=10*x[i][1];
q_1_G_2_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->C5_serial)
{
q_1_G_2_matrix[3][0]=10*x[i][0];
q_1_G_2_matrix[3][1]=10*x[i][1];
q_1_G_2_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->C6_serial)
{
q_1_G_2_matrix[4][0]=10*x[i][0];
q_1_G_2_matrix[4][1]=10*x[i][1];
q_1_G_2_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->C8_serial)
{
q_1_G_2_matrix[1][0]=10*x[i][0];
q_1_G_2_matrix[1][1]=10*x[i][1];
q_1_G_2_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->N1_serial)
{
q_1_G_2_matrix[5][0]=10*x[i][0];
q_1_G_2_matrix[5][1]=10*x[i][1];
q_1_G_2_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->N3_serial)
{
q_1_G_2_matrix[7][0]=10*x[i][0];
q_1_G_2_matrix[7][1]=10*x[i][1];
q_1_G_2_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->N7_serial)
{
q_1_G_2_matrix[2][0]=10*x[i][0];
q_1_G_2_matrix[2][1]=10*x[i][1];
q_1_G_2_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_2->N9_serial)
{
q_1_G_2_matrix[0][0]=10*x[i][0];
q_1_G_2_matrix[0][1]=10*x[i][1];
q_1_G_2_matrix[0][2]=10*x[i][2];
}
//q_1_G_3
if((i+1)==bs_q_1_G_3->C2_serial)
{
q_1_G_3_matrix[6][0]=10*x[i][0];
q_1_G_3_matrix[6][1]=10*x[i][1];
q_1_G_3_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->C4_serial)
{
q_1_G_3_matrix[8][0]=10*x[i][0];
q_1_G_3_matrix[8][1]=10*x[i][1];
q_1_G_3_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->C5_serial)
{
q_1_G_3_matrix[3][0]=10*x[i][0];
q_1_G_3_matrix[3][1]=10*x[i][1];
q_1_G_3_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->C6_serial)
{
q_1_G_3_matrix[4][0]=10*x[i][0];
q_1_G_3_matrix[4][1]=10*x[i][1];
q_1_G_3_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->C8_serial)
{
q_1_G_3_matrix[1][0]=10*x[i][0];
q_1_G_3_matrix[1][1]=10*x[i][1];
q_1_G_3_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->N1_serial)
{
q_1_G_3_matrix[5][0]=10*x[i][0];
q_1_G_3_matrix[5][1]=10*x[i][1];
q_1_G_3_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->N3_serial)
{
q_1_G_3_matrix[7][0]=10*x[i][0];
q_1_G_3_matrix[7][1]=10*x[i][1];
q_1_G_3_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->N7_serial)
{
q_1_G_3_matrix[2][0]=10*x[i][0];
q_1_G_3_matrix[2][1]=10*x[i][1];
q_1_G_3_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_3->N9_serial)
{
q_1_G_3_matrix[0][0]=10*x[i][0];
q_1_G_3_matrix[0][1]=10*x[i][1];
q_1_G_3_matrix[0][2]=10*x[i][2];
}
//q_1_G_4
if((i+1)==bs_q_1_G_4->C2_serial)
{
q_1_G_4_matrix[6][0]=10*x[i][0];
q_1_G_4_matrix[6][1]=10*x[i][1];
q_1_G_4_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->C4_serial)
{
q_1_G_4_matrix[8][0]=10*x[i][0];
q_1_G_4_matrix[8][1]=10*x[i][1];
q_1_G_4_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->C5_serial)
{
q_1_G_4_matrix[3][0]=10*x[i][0];
q_1_G_4_matrix[3][1]=10*x[i][1];
q_1_G_4_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->C6_serial)
{
q_1_G_4_matrix[4][0]=10*x[i][0];
q_1_G_4_matrix[4][1]=10*x[i][1];
q_1_G_4_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->C8_serial)
{
q_1_G_4_matrix[1][0]=10*x[i][0];
q_1_G_4_matrix[1][1]=10*x[i][1];
q_1_G_4_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->N1_serial)
{
q_1_G_4_matrix[5][0]=10*x[i][0];
q_1_G_4_matrix[5][1]=10*x[i][1];
q_1_G_4_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->N3_serial)
{
q_1_G_4_matrix[7][0]=10*x[i][0];
q_1_G_4_matrix[7][1]=10*x[i][1];
q_1_G_4_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->N7_serial)
{
q_1_G_4_matrix[2][0]=10*x[i][0];
q_1_G_4_matrix[2][1]=10*x[i][1];
q_1_G_4_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_1_G_4->N9_serial)
{
q_1_G_4_matrix[0][0]=10*x[i][0];
q_1_G_4_matrix[0][1]=10*x[i][1];
q_1_G_4_matrix[0][2]=10*x[i][2];
}
//q_2_G_1
if((i+1)==bs_q_2_G_1->C2_serial)
{
q_2_G_1_matrix[6][0]=10*x[i][0];
q_2_G_1_matrix[6][1]=10*x[i][1];
q_2_G_1_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->C4_serial)
{
q_2_G_1_matrix[8][0]=10*x[i][0];
q_2_G_1_matrix[8][1]=10*x[i][1];
q_2_G_1_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->C5_serial)
{
q_2_G_1_matrix[3][0]=10*x[i][0];
q_2_G_1_matrix[3][1]=10*x[i][1];
q_2_G_1_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->C6_serial)
{
q_2_G_1_matrix[4][0]=10*x[i][0];
q_2_G_1_matrix[4][1]=10*x[i][1];
q_2_G_1_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->C8_serial)
{
q_2_G_1_matrix[1][0]=10*x[i][0];
q_2_G_1_matrix[1][1]=10*x[i][1];
q_2_G_1_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->N1_serial)
{
q_2_G_1_matrix[5][0]=10*x[i][0];
q_2_G_1_matrix[5][1]=10*x[i][1];
q_2_G_1_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->N3_serial)
{
q_2_G_1_matrix[7][0]=10*x[i][0];
q_2_G_1_matrix[7][1]=10*x[i][1];
q_2_G_1_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->N7_serial)
{
q_2_G_1_matrix[2][0]=10*x[i][0];
q_2_G_1_matrix[2][1]=10*x[i][1];
q_2_G_1_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_1->N9_serial)
{
q_2_G_1_matrix[0][0]=10*x[i][0];
q_2_G_1_matrix[0][1]=10*x[i][1];
q_2_G_1_matrix[0][2]=10*x[i][2];
}
//q_2_G_2
if((i+1)==bs_q_2_G_2->C2_serial)
{
q_2_G_2_matrix[6][0]=10*x[i][0];
q_2_G_2_matrix[6][1]=10*x[i][1];
q_2_G_2_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->C4_serial)
{
q_2_G_2_matrix[8][0]=10*x[i][0];
q_2_G_2_matrix[8][1]=10*x[i][1];
q_2_G_2_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->C5_serial)
{
q_2_G_2_matrix[3][0]=10*x[i][0];
q_2_G_2_matrix[3][1]=10*x[i][1];
q_2_G_2_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->C6_serial)
{
q_2_G_2_matrix[4][0]=10*x[i][0];
q_2_G_2_matrix[4][1]=10*x[i][1];
q_2_G_2_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->C8_serial)
{
q_2_G_2_matrix[1][0]=10*x[i][0];
q_2_G_2_matrix[1][1]=10*x[i][1];
q_2_G_2_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->N1_serial)
{
q_2_G_2_matrix[5][0]=10*x[i][0];
q_2_G_2_matrix[5][1]=10*x[i][1];
q_2_G_2_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->N3_serial)
{
q_2_G_2_matrix[7][0]=10*x[i][0];
q_2_G_2_matrix[7][1]=10*x[i][1];
q_2_G_2_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->N7_serial)
{
q_2_G_2_matrix[2][0]=10*x[i][0];
q_2_G_2_matrix[2][1]=10*x[i][1];
q_2_G_2_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_2->N9_serial)
{
q_2_G_2_matrix[0][0]=10*x[i][0];
q_2_G_2_matrix[0][1]=10*x[i][1];
q_2_G_2_matrix[0][2]=10*x[i][2];
}
//q_2_G_3
if((i+1)==bs_q_2_G_3->C2_serial)
{
q_2_G_3_matrix[6][0]=10*x[i][0];
q_2_G_3_matrix[6][1]=10*x[i][1];
q_2_G_3_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->C4_serial)
{
q_2_G_3_matrix[8][0]=10*x[i][0];
q_2_G_3_matrix[8][1]=10*x[i][1];
q_2_G_3_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->C5_serial)
{
q_2_G_3_matrix[3][0]=10*x[i][0];
q_2_G_3_matrix[3][1]=10*x[i][1];
q_2_G_3_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->C6_serial)
{
q_2_G_3_matrix[4][0]=10*x[i][0];
q_2_G_3_matrix[4][1]=10*x[i][1];
q_2_G_3_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->C8_serial)
{
q_2_G_3_matrix[1][0]=10*x[i][0];
q_2_G_3_matrix[1][1]=10*x[i][1];
q_2_G_3_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->N1_serial)
{
q_2_G_3_matrix[5][0]=10*x[i][0];
q_2_G_3_matrix[5][1]=10*x[i][1];
q_2_G_3_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->N3_serial)
{
q_2_G_3_matrix[7][0]=10*x[i][0];
q_2_G_3_matrix[7][1]=10*x[i][1];
q_2_G_3_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->N7_serial)
{
q_2_G_3_matrix[2][0]=10*x[i][0];
q_2_G_3_matrix[2][1]=10*x[i][1];
q_2_G_3_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_3->N9_serial)
{
q_2_G_3_matrix[0][0]=10*x[i][0];
q_2_G_3_matrix[0][1]=10*x[i][1];
q_2_G_3_matrix[0][2]=10*x[i][2];
}
//q_2_G_4
if((i+1)==bs_q_2_G_4->C2_serial)
{
q_2_G_4_matrix[6][0]=10*x[i][0];
q_2_G_4_matrix[6][1]=10*x[i][1];
q_2_G_4_matrix[6][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->C4_serial)
{
q_2_G_4_matrix[8][0]=10*x[i][0];
q_2_G_4_matrix[8][1]=10*x[i][1];
q_2_G_4_matrix[8][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->C5_serial)
{
q_2_G_4_matrix[3][0]=10*x[i][0];
q_2_G_4_matrix[3][1]=10*x[i][1];
q_2_G_4_matrix[3][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->C6_serial)
{
q_2_G_4_matrix[4][0]=10*x[i][0];
q_2_G_4_matrix[4][1]=10*x[i][1];
q_2_G_4_matrix[4][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->C8_serial)
{
q_2_G_4_matrix[1][0]=10*x[i][0];
q_2_G_4_matrix[1][1]=10*x[i][1];
q_2_G_4_matrix[1][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->N1_serial)
{
q_2_G_4_matrix[5][0]=10*x[i][0];
q_2_G_4_matrix[5][1]=10*x[i][1];
q_2_G_4_matrix[5][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->N3_serial)
{
q_2_G_4_matrix[7][0]=10*x[i][0];
q_2_G_4_matrix[7][1]=10*x[i][1];
q_2_G_4_matrix[7][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->N7_serial)
{
q_2_G_4_matrix[2][0]=10*x[i][0];
q_2_G_4_matrix[2][1]=10*x[i][1];
q_2_G_4_matrix[2][2]=10*x[i][2];
}
if((i+1)==bs_q_2_G_4->N9_serial)
{
q_2_G_4_matrix[0][0]=10*x[i][0];
q_2_G_4_matrix[0][1]=10*x[i][1];
q_2_G_4_matrix[0][2]=10*x[i][2];
}
}
double ** q_1_G_1_rotation_matrix;
double ** q_1_G_2_rotation_matrix;
double ** q_1_G_3_rotation_matrix;
double ** q_1_G_4_rotation_matrix;
double ** q_2_G_1_rotation_matrix;
double ** q_2_G_2_rotation_matrix;
double ** q_2_G_3_rotation_matrix;
double ** q_2_G_4_rotation_matrix;
q_1_G_1_rotation_matrix=dmatrix(0,2,0,2);
q_1_G_2_rotation_matrix=dmatrix(0,2,0,2);
q_1_G_3_rotation_matrix=dmatrix(0,2,0,2);
q_1_G_4_rotation_matrix=dmatrix(0,2,0,2);
q_2_G_1_rotation_matrix=dmatrix(0,2,0,2);
q_2_G_2_rotation_matrix=dmatrix(0,2,0,2);
q_2_G_3_rotation_matrix=dmatrix(0,2,0,2);
q_2_G_4_rotation_matrix=dmatrix(0,2,0,2);
Rotation_matrix(q_1_G_1_matrix,'G',q_1_G_1_rotation_matrix);
Rotation_matrix(q_1_G_2_matrix,'G',q_1_G_2_rotation_matrix);
Rotation_matrix(q_1_G_3_matrix,'G',q_1_G_3_rotation_matrix);
Rotation_matrix(q_1_G_4_matrix,'G',q_1_G_4_rotation_matrix);
Rotation_matrix(q_2_G_1_matrix,'G',q_2_G_1_rotation_matrix);
Rotation_matrix(q_2_G_2_matrix,'G',q_2_G_2_rotation_matrix);
Rotation_matrix(q_2_G_3_matrix,'G',q_2_G_3_rotation_matrix);
Rotation_matrix(q_2_G_4_matrix,'G',q_2_G_4_rotation_matrix);
//以q_1_G_1为基准，校正z-axis的方向。
double * vector_q_1_G_1;
double * vector_q_1_G_2;
double * vector_q_1_G_3;
double * vector_q_1_G_4;
double * vector_q_2_G_1;
double * vector_q_2_G_2;
double * vector_q_2_G_3;
double * vector_q_2_G_4;
vector_q_1_G_1=dvector(0,2);
vector_q_1_G_2=dvector(0,2);
vector_q_1_G_3=dvector(0,2);
vector_q_1_G_4=dvector(0,2);
vector_q_2_G_1=dvector(0,2);
vector_q_2_G_2=dvector(0,2);
vector_q_2_G_3=dvector(0,2);
vector_q_2_G_4=dvector(0,2);
for(int i=0;i<3;i++)
{
vector_q_1_G_1[i]=q_1_G_1_rotation_matrix[i][2];
vector_q_1_G_2[i]=q_1_G_2_rotation_matrix[i][2];
vector_q_1_G_3[i]=q_1_G_3_rotation_matrix[i][2];
vector_q_1_G_4[i]=q_1_G_4_rotation_matrix[i][2];
vector_q_2_G_1[i]=q_2_G_1_rotation_matrix[i][2];
vector_q_2_G_2[i]=q_2_G_2_rotation_matrix[i][2];
vector_q_2_G_3[i]=q_2_G_3_rotation_matrix[i][2];
vector_q_2_G_4[i]=q_2_G_4_rotation_matrix[i][2];
}
if(dot_product_vector(vector_q_1_G_1,vector_q_1_G_2,3)<0)
{
for(int i=1;i<3;i++)
{
for(int j=0;j<3;j++)
{
q_1_G_2_rotation_matrix[j][i]= - q_1_G_2_rotation_matrix[j][i];
}
}
}
if(dot_product_vector(vector_q_1_G_1,vector_q_1_G_3,3)<0)
{
for(int i=1;i<3;i++)
{
for(int j=0;j<3;j++)
{
q_1_G_3_rotation_matrix[j][i]= - q_1_G_3_rotation_matrix[j][i];
}
}
}
if(dot_product_vector(vector_q_1_G_1,vector_q_1_G_4,3)<0)
{
for(int i=1;i<3;i++)
{
for(int j=0;j<3;j++)
{
q_1_G_4_rotation_matrix[j][i]= - q_1_G_4_rotation_matrix[j][i];
}
}
}
if(dot_product_vector(vector_q_1_G_1,vector_q_2_G_1,3)<0)
{
for(int i=1;i<3;i++)
{
for(int j=0;j<3;j++)
{
q_2_G_1_rotation_matrix[j][i]= - q_2_G_1_rotation_matrix[j][i];
}
}
}
if(dot_product_vector(vector_q_1_G_1,vector_q_2_G_2,3)<0)
{
for(int i=1;i<3;i++)
{
for(int j=0;j<3;j++)
{
q_2_G_2_rotation_matrix[j][i]= - q_2_G_2_rotation_matrix[j][i];
}
}
}
if(dot_product_vector(vector_q_1_G_1,vector_q_2_G_3,3)<0)
{
for(int i=1;i<3;i++)
{
for(int j=0;j<3;j++)
{
q_2_G_3_rotation_matrix[j][i]= - q_2_G_3_rotation_matrix[j][i];
}
}
}
if(dot_product_vector(vector_q_1_G_1,vector_q_2_G_4,3)<0)
{
for(int i=1;i<3;i++)
{
for(int j=0;j<3;j++)
{
q_2_G_4_rotation_matrix[j][i]= - q_2_G_4_rotation_matrix[j][i];
}
}
}
free_dvector(vector_q_1_G_1,0,2);
free_dvector(vector_q_1_G_2,0,2);
free_dvector(vector_q_1_G_3,0,2);
free_dvector(vector_q_1_G_4,0,2);
free_dvector(vector_q_2_G_1,0,2);
free_dvector(vector_q_2_G_2,0,2);
free_dvector(vector_q_2_G_3,0,2);
free_dvector(vector_q_2_G_4,0,2);
//get the origin position of 8 guanine.
double * origin_vector_q_1_G_1;
double * origin_vector_q_1_G_2;
double * origin_vector_q_1_G_3;
double * origin_vector_q_1_G_4;
double * origin_vector_q_2_G_1;
double * origin_vector_q_2_G_2;
double * origin_vector_q_2_G_3;
double * origin_vector_q_2_G_4;
origin_vector_q_1_G_1=dvector(0,2);
origin_vector_q_1_G_2=dvector(0,2);
origin_vector_q_1_G_3=dvector(0,2);
origin_vector_q_1_G_4=dvector(0,2);
origin_vector_q_2_G_1=dvector(0,2);
origin_vector_q_2_G_2=dvector(0,2);
origin_vector_q_2_G_3=dvector(0,2);
origin_vector_q_2_G_4=dvector(0,2);
origin_vector(q_1_G_1_matrix,q_1_G_1_rotation_matrix,'G',origin_vector_q_1_G_1);
origin_vector(q_1_G_2_matrix,q_1_G_2_rotation_matrix,'G',origin_vector_q_1_G_2);
origin_vector(q_1_G_3_matrix,q_1_G_3_rotation_matrix,'G',origin_vector_q_1_G_3);
origin_vector(q_1_G_4_matrix,q_1_G_4_rotation_matrix,'G',origin_vector_q_1_G_4);
origin_vector(q_2_G_1_matrix,q_2_G_1_rotation_matrix,'G',origin_vector_q_2_G_1);
origin_vector(q_2_G_2_matrix,q_2_G_2_rotation_matrix,'G',origin_vector_q_2_G_2);
origin_vector(q_2_G_3_matrix,q_2_G_3_rotation_matrix,'G',origin_vector_q_2_G_3);
origin_vector(q_2_G_4_matrix,q_2_G_4_rotation_matrix,'G',origin_vector_q_2_G_4);
//get the z-axis
vector_q_1_G_1=dvector(0,2);
vector_q_1_G_2=dvector(0,2);
vector_q_1_G_3=dvector(0,2);
vector_q_1_G_4=dvector(0,2);
vector_q_2_G_1=dvector(0,2);
vector_q_2_G_2=dvector(0,2);
vector_q_2_G_3=dvector(0,2);
vector_q_2_G_4=dvector(0,2);
for(int i=0;i<3;i++)
{
vector_q_1_G_1[i]=q_1_G_1_rotation_matrix[i][2];
vector_q_1_G_2[i]=q_1_G_2_rotation_matrix[i][2];
vector_q_1_G_3[i]=q_1_G_3_rotation_matrix[i][2];
vector_q_1_G_4[i]=q_1_G_4_rotation_matrix[i][2];
vector_q_2_G_1[i]=q_2_G_1_rotation_matrix[i][2];
vector_q_2_G_2[i]=q_2_G_2_rotation_matrix[i][2];
vector_q_2_G_3[i]=q_2_G_3_rotation_matrix[i][2];
vector_q_2_G_4[i]=q_2_G_4_rotation_matrix[i][2];
// cout<<vector_q_1_G_1[i]<<endl; //for test
// cout<<vector_q_1_G_2[i]<<endl; //for test
// cout<<vector_q_1_G_3[i]<<endl; //for test
// cout<<vector_q_1_G_4[i]<<endl; //for test
// cout<<vector_q_2_G_1[i]<<endl; //for test
// cout<<vector_q_2_G_2[i]<<endl; //for test
// cout<<vector_q_2_G_3[i]<<endl; //for test
// cout<<vector_q_2_G_4[i]<<endl; //for test
}
double * vector_q_1_G_1_2;
double * vector_q_1_G_3_4;
double * vector_q_1_G_1_2_3_4;
double * vector_q_2_G_1_2;
double * vector_q_2_G_3_4;
double * vector_q_2_G_1_2_3_4;
double * vector_orientation;
vector_q_1_G_1_2=dvector(0,2);
vector_q_1_G_3_4=dvector(0,2);
vector_q_1_G_1_2_3_4=dvector(0,2);
vector_q_2_G_1_2=dvector(0,2);
vector_q_2_G_3_4=dvector(0,2);
vector_q_2_G_1_2_3_4=dvector(0,2);
vector_orientation=dvector(0,2);
rotate_2_vector(vector_q_1_G_1,vector_q_1_G_2, vector_q_1_G_1_2);
// for test
// for(int i=0;i<3;i++)
// {
// cout<<vector_q_1_G_1_2[i]<<endl;
// }
//
rotate_2_vector(vector_q_1_G_3,vector_q_1_G_4,vector_q_1_G_3_4);
rotate_2_vector(vector_q_2_G_1,vector_q_2_G_2,vector_q_2_G_1_2);
rotate_2_vector(vector_q_2_G_3,vector_q_2_G_4,vector_q_2_G_3_4);
rotate_2_vector(vector_q_1_G_1_2,vector_q_1_G_3_4,vector_q_1_G_1_2_3_4);
rotate_2_vector(vector_q_2_G_1_2,vector_q_2_G_3_4,vector_q_2_G_1_2_3_4);
rotate_2_vector(vector_q_1_G_1_2_3_4,vector_q_2_G_1_2_3_4,vector_orientation);
//for test
/*
for(int i=0;i<3;i++)
{
cout<<vector_orientation[i]<<endl;
}
*/
//
//get the center position.
double * center_position_vector;
double * center_1;
double * center_2;
double * vector_2_ion;
double * vector_1_2;
center_position_vector=dvector(0,2);
vector_2_ion=dvector(0,2);
center_1=dvector(0,2);
center_2=dvector(0,2);
vector_1_2=dvector(0,2);
for(int i=0;i<3;i++)
{
center_position_vector[i]=(origin_vector_q_1_G_1[i]+origin_vector_q_1_G_2[i]+origin_vector_q_1_G_3[i]+origin_vector_q_1_G_4[i]+origin_vector_q_2_G_1[i]+origin_vector_q_2_G_2[i]+origin_vector_q_2_G_3[i]+origin_vector_q_2_G_4[i])/8;
center_1[i]=(origin_vector_q_1_G_1[i]+origin_vector_q_1_G_2[i]+origin_vector_q_1_G_3[i]+origin_vector_q_1_G_4[i])/4;
center_2[i]=(origin_vector_q_2_G_1[i]+origin_vector_q_2_G_2[i]+origin_vector_q_2_G_3[i]+origin_vector_q_2_G_4[i])/4;
vector_2_ion[i]=ion_coor[i]-center_position_vector[i];
vector_1_2[i]=center_1[i]-center_2[i];
}
double length=0;
double dist_z=0;
double dist=0;
length=dot_product_vector(vector_orientation,vector_2_ion,3);
dist_z=dot_product_vector(vector_orientation,vector_1_2,3);
dist=sqrt(dot_product_vector(vector_1_2,vector_1_2,3));
//
out<<fixed<<showpoint;
out<<time_temp<<"\t"<<setprecision(4)<<fabs(length)<<"\t"<<setprecision(4)<<dist<<"\t"<<setprecision(4)<<fabs(dist_z)<<endl;
free_dmatrix(q_1_G_1_matrix,0,2,0,8);
free_dmatrix(q_1_G_2_matrix,0,2,0,8);
free_dmatrix(q_1_G_3_matrix,0,2,0,8);
free_dmatrix(q_1_G_4_matrix,0,2,0,8);
free_dmatrix(q_2_G_1_matrix,0,2,0,8);
free_dmatrix(q_2_G_2_matrix,0,2,0,8);
free_dmatrix(q_2_G_3_matrix,0,2,0,8);
free_dmatrix(q_2_G_4_matrix,0,2,0,8);
free_dmatrix(q_1_G_1_rotation_matrix,0,2,0,2);
free_dmatrix(q_1_G_2_rotation_matrix,0,2,0,2);
free_dmatrix(q_1_G_3_rotation_matrix,0,2,0,2);
free_dmatrix(q_1_G_4_rotation_matrix,0,2,0,2);
free_dmatrix(q_2_G_1_rotation_matrix,0,2,0,2);
free_dmatrix(q_2_G_2_rotation_matrix,0,2,0,2);
free_dmatrix(q_2_G_3_rotation_matrix,0,2,0,2);
free_dmatrix(q_2_G_4_rotation_matrix,0,2,0,2);
free_dvector(vector_q_1_G_1,0,2);
free_dvector(vector_q_1_G_2,0,2);
free_dvector(vector_q_1_G_3,0,2);
free_dvector(vector_q_1_G_4,0,2);
free_dvector(vector_q_2_G_1,0,2);
free_dvector(vector_q_2_G_2,0,2);
free_dvector(vector_q_2_G_3,0,2);
free_dvector(vector_q_2_G_4,0,2);
free_dvector(origin_vector_q_1_G_1,0,2);
free_dvector(origin_vector_q_1_G_2,0,2);
free_dvector(origin_vector_q_1_G_3,0,2);
free_dvector(origin_vector_q_1_G_4,0,2);
free_dvector(origin_vector_q_2_G_1,0,2);
free_dvector(origin_vector_q_2_G_2,0,2);
free_dvector(origin_vector_q_2_G_3,0,2);
free_dvector(origin_vector_q_2_G_4,0,2);
free_dvector(vector_q_1_G_1_2,0,2);
free_dvector(vector_q_1_G_3_4,0,2);
free_dvector(vector_q_1_G_1_2_3_4,0,2);
free_dvector(vector_q_2_G_1_2,0,2);
free_dvector(vector_q_2_G_3_4,0,2);
free_dvector( vector_q_2_G_1_2_3_4,0,2);
free_dvector( vector_orientation,0,2);
}
}
xdrfile_close(xtc);
out.close();
}
