bool XtcLoader:: reinit (const char * filename) { char tmpname[2048]; strncpy (tmpname, filename, 2047); xd = xdrfile_open (filename, "r"); if (xd == NULL){ std::cerr << "cannot open file " << filename << std::endl; return false; } read_xtc_natoms (tmpname, &natoms); step = 0; time = 0.; box = vector<double > (3, 0.); xx = (rvec *) malloc (sizeof(rvec) * natoms); prec = 1000.; inited = true; load (); xdrfile_close (xd); xd = xdrfile_open (filename, "r"); if (xd == NULL){ std::cerr << "cannot open file " << filename << std::endl; clear (); return false; } return true; }
/*! * This will open an xtc file for reading. The number of atoms in each frame * is saved and memory for the coordinate array is allocated. */ bool FormatXTC::open(string s) { if (xd!=NULL) close(); xd = xdrfile_open(&s[0], "r"); if (xd!=NULL) { int rc = read_xtc_natoms(&s[0], &natoms_xtc); // get number of atoms if (rc==exdrOK) { x_xtc = new rvec [natoms_xtc]; // resize coordinate array return true; } } else std::cerr << "# ioxtc error: xtc file could not be opened." << endl; return false; }
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(); }
void ReadWrite(char *rfile, char *wfile, int in_xtcBool, int out_xtcBool, int in_trrBool, int out_trrBool) { XDRFILE *xd_read, *xd_write; int result_xtc, result_trr; int natoms_xtc, natoms_trr; int step_xtc, step_trr; float time_xtc, time_trr; matrix box_xtc, box_trr; rvec *x_xtc, *x_trr, *v_trr, *f_trr; float prec_xtc = 1000.0; float lambda_trr = 0.0; xd_read = xdrfile_open(rfile, "r"); if (NULL == xd_read) die("Opening xdrfile for reading"); /* Test whether output file exists */ if ((xd_write = xdrfile_open(wfile,"r")) != NULL) { xdrfile_close(xd_write); die("Output file exists."); } /* Output file does not exist. Now we can open it for writing */ xd_write = xdrfile_open(wfile, "w"); if (NULL == xd_write) die("Opening xdrfile for writing"); /* .xtc -> .xtc */ if(in_xtcBool && out_xtcBool) { result_xtc = read_xtc_natoms(rfile, &natoms_xtc); if (exdrOK != result_xtc) die_r("read_xtc_natoms",result_xtc); x_xtc = (rvec *)calloc(natoms_xtc, sizeof(x_xtc[0])); while(1) { result_xtc = read_xtc(xd_read, natoms_xtc, &step_xtc, &time_xtc, box_xtc, x_xtc, &prec_xtc); if (result_xtc == 0) // if not reach the end of file, write it to the output.xtc file { if (exdrOK != result_xtc) die_r("Reading xtc file", result_xtc); result_xtc = write_xtc(xd_write, natoms_xtc, step_xtc, time_xtc, box_xtc, x_xtc, prec_xtc); if (result_xtc != 0) die_r("Writing xtc file", result_xtc); } else break; } } /* .xtc -> .trr */ if(in_xtcBool && out_trrBool) { result_xtc = read_xtc_natoms(rfile, &natoms_xtc); if (exdrOK != result_xtc) die_r("read_xtc_natoms",result_xtc); x_xtc = (rvec *)calloc(natoms_xtc, sizeof(x_xtc[0])); while(1) { result_xtc = read_xtc(xd_read, natoms_xtc, &step_xtc, &time_xtc, box_xtc, x_xtc, &prec_xtc); if (result_xtc == 0) // if not reach the end of file, write it to the output.trr file { if (exdrOK != result_xtc) die_r("Reading xtc file", result_xtc); result_trr = write_trr(xd_write, natoms_xtc, step_xtc, time_xtc, lambda_trr, box_xtc, x_xtc, NULL, NULL); if (0 != result_trr) die_r("Writing trr file",result_trr); } else break; } } /* .trr -> .trr */ if(in_trrBool && out_trrBool) { result_trr = read_trr_natoms(rfile, &natoms_trr); if (exdrOK != result_trr) die_r("read_trr_natoms",result_trr); x_trr = (rvec *)calloc(natoms_trr, sizeof(x_trr[0])); v_trr = (rvec *)calloc(natoms_trr, sizeof(v_trr[0])); f_trr = (rvec *)calloc(natoms_trr, sizeof(f_trr[0])); while (1) { result_trr = read_trr(xd_read, natoms_trr, &step_trr, &time_trr, &lambda_trr, box_trr, x_trr, v_trr, f_trr); int ii_trr, jj_trr, x_ck=0, v_ck=0, f_ck=0; int x_ck_bool=0, v_ck_bool=0, f_ck_bool=0; for (ii_trr = 0; ii_trr < natoms_trr; ii_trr++) { for(jj_trr = 0; jj_trr < DIM; jj_trr++) { if (x_trr[ii_trr][jj_trr] == 0) x_ck++; if (v_trr[ii_trr][jj_trr] == 0) v_ck++; if (f_trr[ii_trr][jj_trr] == 0) f_ck++; } } if (x_ck == natoms_trr*DIM) x_ck_bool = 1; if (v_ck == natoms_trr*DIM) v_ck_bool = 1; if (f_ck == natoms_trr*DIM) f_ck_bool = 1; if (result_trr == 0) // if not reach the end of file, write it to the output.trr file { if (exdrOK != result_trr) die_r("Reading trr file",result_trr); if(v_ck_bool && f_ck_bool) result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr, box_trr, x_trr, NULL, NULL); else if(v_ck_bool) result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr, box_trr, x_trr, NULL, f_trr); else if(f_ck_bool) result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr, box_trr, x_trr, v_trr, NULL); else result_trr = write_trr(xd_write, natoms_trr, step_trr, time_trr, lambda_trr, box_trr, x_trr, v_trr, f_trr); if (0 != result_trr) die_r("Writing trr file",result_trr); } else break; } } /* .trr -> .xtc */ if(in_trrBool && out_xtcBool) { result_trr = read_trr_natoms(rfile, &natoms_trr); if (exdrOK != result_trr) die_r("read_trr_natoms",result_trr); x_trr = (rvec *)calloc(natoms_trr, sizeof(x_trr[0])); v_trr = (rvec *)calloc(natoms_trr, sizeof(v_trr[0])); f_trr = (rvec *)calloc(natoms_trr, sizeof(f_trr[0])); while(1) { result_trr = read_trr(xd_read, natoms_trr, &step_trr, &time_trr, &lambda_trr, box_trr, x_trr, v_trr, f_trr); if (result_trr == 0) // if not reach the end of file, write it to the output.trr file { if (exdrOK != result_trr) die_r("Reading trr file", result_trr); result_xtc = write_xtc(xd_write, natoms_trr, step_trr, time_trr, box_trr, x_trr, prec_xtc); if (result_xtc != 0) die_r("Writing xtc file", result_xtc); } else break; } } xdrfile_close(xd_read); xdrfile_close(xd_write); }
int main(int argc, char * argv[]) { ValueType begin, end, rup, refh, cellSize; std::string ifile, ofile, method; ValueType x0, x1; po::options_description desc ("Allow options"); desc.add_options() ("help,h", "print this message") ("begin,b", po::value<ValueType > (&begin)->default_value(0.f), "start time") ("end,e", po::value<ValueType > (&end )->default_value(0.f), "end time") ("x0", po::value<ValueType > (&x0)->default_value(0.f), "lower bound of the interval") ("x1", po::value<ValueType > (&x1)->default_value(1.f), "upper bound of the interval, if x1 == 0, use the whole box") ("rup,u", po::value<ValueType > (&rup)->default_value(3.f), "max r to make rdf") ("refh", po::value<ValueType > (&refh)->default_value(0.01f), "bin size") ("cell-size,c", po::value<ValueType > (&cellSize)->default_value(1.f), "cell list radius") ("method,m", po::value<std::string > (&method)->default_value ("adress"), "type of simulation to analyze") ("input,f", po::value<std::string > (&ifile)->default_value ("traj.xtc"), "the input .xtc file") ("output,o", po::value<std::string > (&ofile)->default_value ("rdf.out"), "the output file"); po::variables_map vm; po::store(po::parse_command_line(argc, argv, desc), vm); po::notify (vm); if (vm.count("help")){ std::cout << desc<< "\n"; return 0; } if (x0 > x1) { ValueType tmpx = x0; x0 = x1; x1 = tmpx; } std::cout << "###################################################" << std::endl; std::cout << "# begin->end: " << begin << " " << end << std::endl; std::cout << "# [x0, x1 ]: " << x0 << " " << x1 << std::endl; std::cout << "# rup: " << rup << std::endl; std::cout << "# refh: " << refh << std::endl; std::cout << "# method: " << method << std::endl; std::cout << "# input: " << ifile << std::endl; std::cout << "###################################################" << std::endl; XDRFILE *fp; int natoms, step; float time; matrix box; rvec * xx; float prec = 1000; float time_prec = .01; char tmpfname[1024]; strncpy (tmpfname, ifile.c_str(), 1023); int c; if ((c = read_xtc_natoms (tmpfname, &natoms)) == 0) { // printf ("%d %d\n", c, natoms); xx = (rvec *) malloc (sizeof(rvec) * natoms); } else { // printf ("%d %d\n", c, natoms); fprintf (stderr, "error read_xtc_natoms"); exit (1); } fp = xdrfile_open (ifile.c_str(), "r"); if (fp == NULL){ std::cerr << "cannot open file " << ifile << std::endl; exit (1); } if (read_xtc (fp, natoms, &step, &time, box, xx, &prec) != 0) { std::cerr << "error reading file " << ifile << std::endl; return 1; } int nmolecules = 0; if (method == std::string("adress")){ nmolecules = natoms / 4; } else if (method == std::string("atom")){ nmolecules = natoms / 3; } else if (method == std::string("cg")){ nmolecules = natoms; } else { std::cerr << "wrong method" << std::endl; return 1; } VectorType vbox; vbox.x = box[0][0]; vbox.y = box[1][1]; vbox.z = box[2][2]; if (cellSize >= .5 * vbox.x){ std::cerr << "the cell size should be less than half of the box size" << std::endl; return 1; } std::vector<std::vector<ValueType > > coms; coms.reserve (nmolecules); CellList clist (nmolecules, vbox, cellSize); Rdf myrdf; myrdf.reinit (rup, refh, x0, x1); int countread = 0; while (read_xtc (fp, natoms, &step, &time, box, xx, &prec) == 0){ if (end != 0.f) { if (time < begin - time_prec){ continue; } else if (time > end + time_prec) { break; } } else { if (time < begin - time_prec) continue; } if (countread++ % 1 == 0){ printf ("# load frame at time: %.1f ps\r", time); fflush (stdout); } coms.clear (); if (method == std::string ("adress")){ int nmol = natoms / 4; for (int i = 0; i < nmol; ++i){ if (xx[i*4+3][0] < 0 ) xx[i*4+3][0] += box[0][0]; else if (xx[i*4+3][0] >= box[0][0]) xx[i*4+3][0] -= box[0][0]; if (xx[i*4+3][1] < 0 ) xx[i*4+3][1] += box[1][1]; else if (xx[i*4+3][1] >= box[1][1]) xx[i*4+3][1] -= box[1][1]; if (xx[i*4+3][2] < 0 ) xx[i*4+3][2] += box[2][2]; else if (xx[i*4+3][2] >= box[2][2]) xx[i*4+3][2] -= box[2][2]; std::vector<ValueType > tmp(3); tmp[0] = xx[i*4+3][0]; tmp[1] = xx[i*4+3][1]; tmp[2] = xx[i*4+3][2]; coms.push_back(tmp); } } else if (method == std::string ("atom")){ int nmol = natoms / 3; for (int i = 0; i < nmol; ++i){ std::vector<ValueType > com(3, 0.); for (int dd = 0; dd < 3; ++dd){ ValueType dx1, dx2; dx1 = xx[i*3+1][dd] - xx[i*3+0][dd]; dx2 = xx[i*3+2][dd] - xx[i*3+0][dd]; if (dx1 > 0.5 * box[dd][dd]) {dx1 -= box[dd][dd]; printf ("hit\n");} if (dx1 <-0.5 * box[dd][dd]) {dx1 += box[dd][dd]; printf ("hit\n");} if (dx2 > 0.5 * box[dd][dd]) {dx2 -= box[dd][dd]; printf ("hit\n");} if (dx2 <-0.5 * box[dd][dd]) {dx2 += box[dd][dd]; printf ("hit\n");} com[dd] = 16. * xx[i*3+0][dd] + 1. * (xx[i*3+0][dd] + dx1) + 1. * (xx[i*3+0][dd] + dx2); com[dd] /= 18.; if (com[dd] < 0 ) com[dd] += box[dd][dd]; else if (com[dd] >= box[dd][dd]) com[dd] -= box[dd][dd]; } coms.push_back (com); } } else if (method == std::string ("cg")){ int nmol = natoms; for (int i = 0; i < nmol; ++i){ if (xx[i][0] < 0 ) xx[i][0] += box[0][0]; else if (xx[i][0] >= box[0][0]) xx[i][0] -= box[0][0]; if (xx[i][1] < 0 ) xx[i][1] += box[1][1]; else if (xx[i][1] >= box[1][1]) xx[i][1] -= box[1][1]; if (xx[i][2] < 0 ) xx[i][2] += box[2][2]; else if (xx[i][2] >= box[2][2]) xx[i][2] -= box[2][2]; std::vector<ValueType > tmp(3); tmp[0] = xx[i][0]; tmp[1] = xx[i][1]; tmp[2] = xx[i][2]; coms.push_back(tmp); } } clist.rebuild (coms); myrdf.deposit (coms, vbox, clist); } printf ("\n"); xdrfile_close (fp); free (xx); myrdf.calculate(); FILE *fout = fopen (ofile.c_str(), "w"); if (fout == NULL){ std::cerr << "cannot open file " << ofile << std::endl; exit (1); } fprintf (fout, "%f %f\n", 0., myrdf.getValue(0)); for (unsigned i = 1; i < myrdf.getN(); ++i){ fprintf (fout, "%f %f\n", (i) * refh, myrdf.getValue(i)); } fclose (fout); return 0; }
vector<double> read_xtc2dist(char * filename,vector<int> serial_1,vector<int> serial_2,vector<double> mass_1,vector<double> mass_2) { int natoms,step; float time_temp; float p; vector<double> coor_x; vector<double> coor_y; vector<double> coor_z; vector<double> result; matrix box; rvec *x; XDRFILE *xtc; xtc=xdrfile_open(filename,"r"); int read_return=read_xtc_natoms(filename,&natoms); x=(rvec * )calloc(natoms,sizeof(x[0])); while(1) { read_return=read_xtc(xtc,natoms,&step,&time_temp,box,x,&p); if(step%100000==0) { cout<<"Reading frame"<<"\t"<<step<<" time "<<time_temp<<endl; } if(read_return!=0) { break; } coor_x.clear(); coor_y.clear(); coor_z.clear(); for(int i=0;i<serial_1.size();i++) { // cout<<step<<"\t"<<time_temp<<"\t"<<natom<<"\t"<<x[natom][0]<<"\t"<<x[natom][1]<<"\t"<<x[natom][2]<<endl; int natom=serial_1.at(i); coor_x.push_back(x[natom][0]); coor_y.push_back(x[natom][1]); coor_z.push_back(x[natom][2]); } vector<double> cent_1 =get_center(coor_x,coor_y,coor_z,mass_1); coor_x.clear(); coor_y.clear(); coor_z.clear(); for(int i=0;i<serial_2.size();i++) { int natom=serial_2.at(i); coor_x.push_back(x[natom][0]); coor_y.push_back(x[natom][1]); coor_z.push_back(x[natom][2]); } vector<double> cent_2 =get_center(coor_x,coor_y,coor_z,mass_2); double dist_temp=get_dist(cent_1,cent_2); result.push_back(time_temp); result.push_back(dist_temp); } xdrfile_close(xtc); return result; }
static void test_xtc() { char *testfn = "test.xtc"; XDRFILE *xd; int result,i,j,k,nframes=13; int natoms2,natoms1=173; int step2,step1=1993; float time2,time1=1097.23; matrix box2,box1; rvec *x2,*x1; float prec2,prec1=1000; float toler=1e-3; printf("Testing xtc functionality:"); for(i=0; (i<DIM); i++) for(j=0; (j<DIM); j++) box1[i][j] = (i+1)*3.7 + (j+1); x1 = calloc(natoms1,sizeof(*x1)); if (NULL == x1) die("Allocating memory for x1 in test_xtc"); for(i=0; (i<natoms1); i++) for(j=0; (j<DIM); j++) x1[i][j] = (i+1)*3.7 + (j+1); xd = xdrfile_open(testfn,"w"); if (NULL == xd) die("Opening xdrfile for writing"); for(k=0; (k<nframes); k++) { result = write_xtc(xd,natoms1,step1+k,time1+k,box1,x1,prec1); if (0 != result) die_r("Writing xtc file",result); } xdrfile_close(xd); result = read_xtc_natoms(testfn,&natoms2); if (exdrOK != result) die_r("read_xtc_natoms",result); if (natoms2 != natoms1) die("Number of atoms incorrect when reading trr"); x2 = calloc(natoms2,sizeof(x2[0])); if (NULL == x2) die("Allocating memory for x2"); xd = xdrfile_open(testfn,"r"); if (NULL == xd) die("Opening xdrfile for reading"); k = 0; do { result = read_xtc(xd,natoms2,&step2,&time2,box2,x2,&prec2); if (exdrENDOFFILE != result) { if (exdrOK != result) die_r("read_xtc",result); if (natoms2 != natoms1) die("natoms2 != natoms1"); if (step2-step1 != k) die("incorrect step"); if (fabs(time2-time1-k) > toler) die("incorrect time"); if (fabs(prec2-prec1) > toler) die("incorrect precision"); for(i=0; (i<DIM); i++) for(j=0; (j<DIM); j++) if (fabs(box2[i][j] - box1[i][j]) > toler) die("box incorrect"); for(i=0; (i<natoms1); i++) for(j=0; (j<DIM); j++) if (fabs(x2[i][j] - x1[i][j]) > toler) die("x incorrect"); } k++; } while (result == exdrOK); xdrfile_close(xd); #ifdef HAVE_UNISTD unlink(testfn); #endif printf(" PASSED\n"); }