/export/zimmerman/mjafari/ners590-project/fresh-copy/molecularGSM/GSM/icoord.h Source File

00001 #ifndef ICOORD_H
00002 #define ICOORD_H
00003 
00004 #include "stringtools.h"
00005 #include "pTable.h"
00006 #include "grad.h"
00007 
00008 class ICoord {
00009 
00010   private:
00011 
00012   //move gradient back to private!
00013     int g_inited;
00014 
00015 //    int* atypes;                  //array of MM atom types  
00016     double* amasses;              //array of atomic masses
00017     double* amasses3;
00018 //    double* charge;               //array of MM atomic charges
00019 //    string comment;
00020     double* dxm1;
00021 
00022    //stepsize controllers
00023     double dEpre; 
00024     double smag; 
00025 
00026     int** imptor;
00027 
00028     int nfrags;
00029     int* frags;
00030 
00031     int max_bonds;
00032     int max_angles;
00033     int max_torsions;
00034     int max_imptor;
00035 
00036     int max_nonbond;
00037     int n_nonbond;
00038     int** nonbond;
00039     double* nonbondd;
00040 
00041   void structure_read(string xyzfile);
00042   void alloc_mem();
00043   void make_bonds();
00044   void coord_num();
00045   void make_angles();
00046   void make_torsions();
00047 
00048   void make_frags();
00049   void bond_frags();
00050   void hbond_frags();
00051   void linear_ties();
00052   void h2o_torsions();
00053   void tm_ties();
00054 
00055   void make_imptor(); 
00056 // ic creation function when bonds are already made
00057   void make_imptor_nobonds(); 
00058 
00059   int make_nonbond();
00060 
00061 //
00062   void update_bonds();
00063   void update_angles();
00064   void update_torsion();
00065   void update_imptor();
00066   void update_nonbond();
00067 
00068   void create_xyz();
00069 
00070   double close_bond(int i);
00071   double close_angle(int i);
00072   double close_tor(int i);
00073   int ixflag;
00074 
00075   // MM force field params
00076   double* ffR;
00077   double* ffeps;
00078   double ffbondd(int i, int j);
00079   double ffbonde(int i, int j);
00080   double ffangled(int i, int j);
00081   double ffanglee(int i, int j);
00082   double fftord(int i, int j, int k, int l); 
00083   double fftore(int i, int j, int k, int l); 
00084   double fftorm(int i, int j, int k, int l); //multiplicity 
00085   double ffimptore(int i, int j, int k, int l); 
00086   double ffimptord(int i, int j, int k, int l); 
00087   // function to make arrays?
00088 
00089   int isTM(int anum);
00090 
00091   // Gradient terms
00092   double* bmat;
00093   double* bmatti;
00094 
00095   void print_grad();
00096   void print_gradq();
00097   void bond_grad_all();
00098   void bond_grad_1(int i, int j);
00099   double bond_stretch(int i, int j);
00100   void angle_grad_all();
00101   void angle_grad_1(int i, int j, int k);
00102   void torsion_grad_all();
00103   void torsion_grad_1(int i, int j, int k, int l);
00104   void imptor_grad_all();
00105   void imptor_grad_1(int i, int j, int k, int l);
00106   void vdw_grad_all();
00107   void vdw_grad_1(int i, int j, double scale);
00108 
00109   //Optimizer
00110   //void update_ic_sd();
00111   //void update_ic_cg();
00112   void update_ic_qn();
00113   void update_ic_eigen();
00114   void update_ic_eigen_h(double* C, double* D);
00115   void update_ic_eigen_ts(double* C);
00116   void walk_up();
00117 
00118   void force_notbonds();
00119 
00120   void bmatp_dqbdx(int a1, int a2, double* dqbdx);
00121   void bmatp_dqadx(int a1, int a2, int a3, double* dqadx);
00122   void bmatp_dqtdx(int a1, int a2, int a3, int a4, double* dqtdx);
00123 
00124 //  ofstream xyzfile;
00125   void print_xyzf(ofstream xyzfile); // print xyz coords to file
00126 
00127  //for avoiding regions of space
00128   int nnodes;
00129   double prima_force();
00130   double* prima;
00131   int* aprima;
00132   double* Cp;
00133   double mdist;
00134   void lin_grad_1(int i, int j, double scale);
00135 
00136   char* sbuff;
00137 
00138   double* Gmh; //Gm^1/2
00139   double* Gmih; //Gm^-1/2
00140   void get_gm();
00141   void create_mwHint_EV(double* Lm, double* Lme);
00142  
00143 
00144   public:
00145 
00146   int revertOpt;
00147   Gradient grad1;
00148   string printout;
00149 
00150   double FMAG;
00151   double OPTTHRESH;
00152   double MAXAD;
00153   double DMAX;
00154   double DMIN0;
00155   double SCALEQN0;
00156   double SCALEQN;
00157 
00158   double V0;
00159   int* frozen;
00160 
00161   double farBond;
00162   int isTSnode;
00163   int nneg;
00164   int newHess;
00165   int optCG;
00166   int do_bfgs;
00167   int noptdone;
00168   double path_overlap;
00169   int path_overlap_n;
00170   double path_overlap_e_g;
00171   void update_bfgs();
00172   void update_bfgsp(int makeHint);
00173   void update_bofill();
00174   void save_hess();
00175 
00176   double getR(int i);
00177 
00178   int nicd;
00179     int nicd0; //before constraint applied
00180 
00181     double* bondd;
00182     double* anglev;
00183     double* torv;
00184     double* torv0;
00185     double* torfix;
00186     double* imptorv;
00187 
00188   int** bonds;
00189   int nbonds;
00190   int** angles;
00191   int nangles;
00192   int** torsions;
00193   int ntor;
00194 
00195   double* grad;
00196  // double* pgrad;
00197   double* gradq;
00198   double* pgradq;
00199   double* gradqprim;
00200   double* pgradqprim;
00201   double* dq0;
00202   double* dqm1;
00203   double* dqprim;
00204   double* Hint;
00205   double* Hintp;
00206   double* Hinv;
00207   double* q;
00208   int useExactH;
00209   int isOpt;
00210   int stage1opt;
00211   double pgradrms;
00212   double gradrms;
00213   void make_Hint();
00214   void Hintp_to_Hint();
00215   int davidson_H(int neigen);
00216   int isDavid;
00217 
00218   int id; //for geoms[id] in zstruct
00219   int pid; // previous structure id
00220 
00221   int natoms;
00222   double* coords;
00223   double* coordsts;
00224   double* coords0;
00225   string* anames;               //array of atomic symbols 
00226   int* anumbers;                //array of atomic indices 
00227   int* coordn;                  //coordination number
00228   int nimptor;
00229 
00230   int ic_create();
00231   int ic_create_nobonds();
00232   int mm_grad();
00233   int mm_grad(ICoord shadow);
00234   int grad_to_q();
00235   int ic_to_xyz();
00236   int ic_to_xyz_opt();
00237 //  int qchem_init(string infilename, int ncpu, int run, int rune);
00238   int grad_init(string infilename, int ncpu, int run, int rune, int use_knnr, int q1);
00239   string runends;
00240   string runend2;
00241 
00242   double* bmatp; // in primitives
00243   int get_tangent();
00244   int distance_matrix_ic(ICoord ic1, ICoord ic2);
00245   int union_ic(ICoord ic1, ICoord ic2);
00246   int copy_ic(ICoord ic1);
00247   void write_ic(string filename);
00248   int read_ics(string filename);
00249 
00250   int opt();
00251   int opt(string xyzfile, ICoord shadow);
00252   int opt(string xyzfile);
00253   void opt_constraint(double* C);
00254   double opt_a(int nnewb, int* newb, int nnewt, int* newt, string xyzfile_string, int nsteps);
00255   double opt_b(string xyzfile_string, int nsteps);
00256   double opt_c(string xyzfile_string, int nsteps, double* C, double* C0);
00257   double opt_r(string xyzfile_string, int nsteps, double* C, double* C0, double* D, int type);
00258   double opt_eigen_ts(string xyzfile_string, int nsteps, double* C, double* C0);
00259   void update_ic();
00260   void mm_init();
00261 
00262   int bmat_alloc();
00263   int bmat_free();
00264   int bmatp_finite();
00265   int bmatp_create();
00266   int bmatp_to_U();
00267   int bmat_create();
00268 
00269   double* Ut;
00270   double* Ut0;
00271 
00272 // help functions for iso
00273   int bond_exists(int b1, int b2);
00274   int bond_num(int b1, int b2);
00275   int angle_num(int b1, int b2, int b3);
00276   int tor_num(int b1, int b2, int b3, int b4);
00277   int hpair(int a1, int a2);
00278   int h2count();
00279 
00280   int same_struct(double* xyz);
00281 
00282   int init(string xyzfile);
00283   int init(int natoms, string* anames, int* anumbers, double* xyz);
00284   int alloc(int size); 
00285   int reset(int natoms, string* anames, int* anumbers, double* xyz);
00286   int reset(double* xyz);
00287   void print_q();
00288   void print_ic();
00289   void print_bonds();
00290   void print_xyz();
00291   void print_xyz_save(string filename);
00292   void print_xyz_save(string xyzfile_string, double energy);
00293 
00294 
00295   double distance(int i, int j);
00296   double angle_val(int i, int j, int k);
00297   double torsion_val(int i, int j, int k, int l); // for imptor and torsion
00298 
00299   void freemem();
00300 
00301  //for Hessian tangent
00302   int use_constraint;
00303   int ridge;
00304 
00305   int create_prima(int nnodes, int nbonds, int nangles, int ntor, double** tangents);
00306   void save_hesspu(string filename); 
00307   void save_hessp(string filename);
00308   void read_hessp(string filename);
00309   void read_hessxyz(string filename, int write);
00310 
00311 };
00312 
00313 
00314 
00315 #endif
00316