| 1 |
gilbertke |
103 |
#define EXTERN extern
|
| 2 |
|
|
|
| 3 |
|
|
#include "pcwin.h"
|
| 4 |
|
|
#include "pcmod.h"
|
| 5 |
|
|
|
| 6 |
|
|
#include "angles.h"
|
| 7 |
|
|
#include "attached.h"
|
| 8 |
|
|
#include "energies.h"
|
| 9 |
|
|
#include "bonds_ff.h"
|
| 10 |
|
|
#include "derivs.h"
|
| 11 |
|
|
#include "hess.h"
|
| 12 |
|
|
#include "utility.h"
|
| 13 |
|
|
#include "cutoffs.h"
|
| 14 |
|
|
#include "nonbond.h"
|
| 15 |
|
|
#include "torsions.h"
|
| 16 |
|
|
|
| 17 |
|
|
EXTERN struct t_strbnd {
|
| 18 |
|
|
int nstrbnd, isb[MAXANG][3];
|
| 19 |
|
|
float ksb1[MAXANG],ksb2[MAXANG];
|
| 20 |
|
|
} strbnd;
|
| 21 |
|
|
|
| 22 |
|
|
EXTERN struct t_minim_control {
|
| 23 |
|
|
int type, method, field, added_const;
|
| 24 |
|
|
char added_path[256],added_name[256];
|
| 25 |
|
|
} minim_control;
|
| 26 |
|
|
|
| 27 |
|
|
EXTERN struct t_minim_values {
|
| 28 |
|
|
int iprint, ndc, nconst;
|
| 29 |
|
|
float dielc;
|
| 30 |
|
|
} minim_values;
|
| 31 |
|
|
struct t_solvent {
|
| 32 |
|
|
int type;
|
| 33 |
|
|
double EPSin, EPSsolv;
|
| 34 |
|
|
double doffset, p1,p2,p3,p4,p5;
|
| 35 |
|
|
double *shct,*asolv,*rsolv,*vsolv,*gpol,*rborn;
|
| 36 |
|
|
} solvent;
|
| 37 |
|
|
|
| 38 |
|
|
int Missing_constants;
|
| 39 |
|
|
EXTERN double hesscut;
|
| 40 |
|
|
|
| 41 |
|
|
void message_alert(char *,char *);
|
| 42 |
|
|
void pcm7_min(void);
|
| 43 |
|
|
int initialise(void);
|
| 44 |
|
|
void attach(void);
|
| 45 |
|
|
void get_bonds(void);
|
| 46 |
|
|
void get_angles(void);
|
| 47 |
|
|
void get_torsions(void);
|
| 48 |
|
|
void set_field(int);
|
| 49 |
|
|
double energy(void);
|
| 50 |
|
|
double get_total_energy(void);
|
| 51 |
|
|
double get_total_deriv_x(int i);
|
| 52 |
|
|
double get_total_deriv_y(int i);
|
| 53 |
|
|
double get_total_deriv_z(int i);
|
| 54 |
|
|
double print_energy(void);
|
| 55 |
|
|
void set_active(void);
|
| 56 |
|
|
int setup_calculation(void);
|
| 57 |
|
|
void end_calculation(void);
|
| 58 |
|
|
|
| 59 |
|
|
void ebond(int nbnd,int (*)[2],int *type,int *tclass,int *use,double *x,double *y,double *z,double *bl,double *bk,double *estr);
|
| 60 |
|
|
void ebond1(int natom,int nbnd,int (*)[2],int *type,int *tclass,int *use,double *x,double *y,double *z,double *bl,double *bk,double *estr,double **deb);
|
| 61 |
|
|
void eangle(int nang,int (*)[4],int *use,double *x,double *y,double *z,int *angin,int *angtype,float *anat,float *acon,double *ebend);
|
| 62 |
|
|
void eangle1(int nang,int natom,int (*)[4],int *use,double *x,double *y,double *z,int *angin,int *angtype,float *anat,float *acon,double *ebend,double **dea);
|
| 63 |
|
|
void ebufcharge(int natom,int *use,int **skip,double *x,double *y,double *z,double *charge,double chrgcut,double *eu);
|
| 64 |
|
|
void ebufcharge1(int natom,int *use,int **skip,double *x,double *y,double *z,double *charge,double chrgcut,double *eu,double **deqq);
|
| 65 |
|
|
void ehal(int natom,int *type,int *use,double *x,double *y,double *z,double vdwcut,int **skip,double **vrad,double **veps,double *evdw,double *e14);
|
| 66 |
|
|
void ehal1(int natom,int *type,int *use,double *x,double *y,double *z,double vdwcut,int **skip,double **vrad,double **veps,double *evdw,double *e14,
|
| 67 |
|
|
double **devdw,double **de14);
|
| 68 |
|
|
void etorsion(int ntor,int **i14,int *use,int *type,double *x,double *y,double *z,int *phin1,int *phin2,int *phin3,int *phin4,int *phin5,int *phin6,float *vin1,float *vin2,
|
| 69 |
|
|
float *vin3,float *vin4,float *vin5,float *vin6,double *etor);
|
| 70 |
|
|
void etorsion1(int natom,int ntor,int **i14,int *use,double *x,double *y,double *z,int *phin1,int *phin2,int *phin3,int *phin4,int *phin5,int *phin6,float *vin1,float *vin2,
|
| 71 |
|
|
float *vin3,float *vin4,float *vin5,float *vin6,double *etor,double **detor);
|
| 72 |
|
|
void eopbend_wilson(int nang,int (*)[4],int *use,double *x,double *y,double *z,int *angin,float *copb,double *eopb);
|
| 73 |
|
|
void eopbend_wilson1(int natom,int nang,int (*)[4],int *use,double *x,double *y,double *z,int *angin,float *copb,double *eopb,double **deopb);
|
| 74 |
|
|
void estrbnd(int nstrbnd,int (*)[3],int (*)[4],int *use,double *x,double *y,double *z,float *anat,double *bl,double *bk,float *ksb1,
|
| 75 |
|
|
float *ksb2,double *estrbnd);
|
| 76 |
|
|
void estrbnd1(int natom,int nstrbnd,int (*)[3],int (*)[4],int *use,double *x,double *y,double *z,float *anat,double *bl,double *bk,float *ksb1,
|
| 77 |
|
|
float *ksb2,double *estrbnd,double **destb);
|
| 78 |
|
|
void egeom(int natom,int *use,double *x,double *y,double *z,double *egeom);
|
| 79 |
|
|
void egeom1(int natom,int *use,double *x,double *y,double *z,double *egeom,double **degeom);
|
| 80 |
|
|
void esolv(int natom,double chrgcut,int **skip,int *mmx_type,int *use,double *charge,double *x,double *y,double *z,double *esolv);
|
| 81 |
|
|
void esolv1(int natom,double chrgcut,int **skip,int *mmx_type,int *use,double *charge,double *x,double *y,double *z,double *esolv,double **desolv,double *drb);
|
| 82 |
|
|
|
| 83 |
|
|
void hessian(int, double *,int *, int *, int *,double *);
|
| 84 |
gilbertke |
104 |
void ebond2(int ia,int (*)[2],int **,int **,double *x,double *y,double *z,double *bl,double *bk,float **hessx,float **hessy,float **hessz);
|
| 85 |
gilbertke |
103 |
void eangle2(int i,int nang,int (*)[4],int *angin, double *x,double *y,double *z,float *acon,float *anat,double **dea,float **hessx,float **hessy,float **hessz);
|
| 86 |
|
|
void etorsion2(int iatom,int ntor,int **i14,int *use,double *x,double *y,double *z,int *phin1,int *phin2,int *phin3,int *phin4,int *phin5,int *phin6,float *vin1,float *vin2,
|
| 87 |
|
|
float *vin3,float *vin4,float *vin5,float *vin6,float **hessx,float **hessy,float **hessz);
|
| 88 |
|
|
void ehal2(int iatom,int natom,int *type,int *use,double *x,double *y,double *z,double vdwcut,int **skip,double **vrad,double **veps,
|
| 89 |
|
|
float **hessx,float **hessy,float **hessz);
|
| 90 |
|
|
void ebufcharge2(int i,int natom,int *use,int **skip,double *x,double *y,double *z,double *charge,double chrgcut,float **hessx,float **hessy,float **hessz);
|
| 91 |
|
|
void eopbend_wilson2(int i,int nang,int (*)[4],int *use,double *x,double *y,double *z,int *angin,float *copb,
|
| 92 |
|
|
float **hessx,float **hessy,float **hessz);
|
| 93 |
|
|
void estrbnd2(int iatom,int nstrbnd,int (*)[3],int (*)[4],int *use,double *x,double *y,double *z,float *anat,double *bl,double *bk,float *ksb1,
|
| 94 |
|
|
float *ksb2,float **hessx,float **hessy,float **hessz);
|
| 95 |
|
|
void esolv2(int ia,int natom,double chrgcut,int *mmx_type,double *charge,double *x,double *y,double *z,float **hessx,float **hessy,float **hessz);
|
| 96 |
|
|
void egeom2(int ,int natom,int *use,double *x,double *y,double *z,float **hessx,float **hessy,float **hessz);
|
| 97 |
|
|
|
| 98 |
|
|
void kangle(void);
|
| 99 |
|
|
void ktorsion(void);
|
| 100 |
|
|
void kstrbnd(void);
|
| 101 |
|
|
void kcharge(void);
|
| 102 |
|
|
void ksolv(void);
|
| 103 |
|
|
void kopbend(void);
|
| 104 |
|
|
void kvdw(void);
|
| 105 |
|
|
int kbond(void);
|
| 106 |
|
|
|
| 107 |
|
|
void get_memory(void);
|
| 108 |
|
|
void free_memory(void);
|
| 109 |
|
|
void gradient(void);
|
| 110 |
|
|
void read_datafiles(char *);
|
| 111 |
|
|
void get_added_const(void);
|
| 112 |
|
|
void hdel(int);
|
| 113 |
|
|
void set_atomtypes(int);
|
| 114 |
|
|
void type(void);
|
| 115 |
|
|
void zero_data(void);
|
| 116 |
|
|
void potoff(void);
|
| 117 |
|
|
int use_bond(void);
|
| 118 |
|
|
int use_angle(void);
|
| 119 |
|
|
int use_strbnd(void);
|
| 120 |
|
|
int use_opbend_wilson(void);
|
| 121 |
|
|
int use_tors(void);
|
| 122 |
|
|
int use_strtor(void);
|
| 123 |
|
|
int use_hal(void);
|
| 124 |
|
|
int use_charge(void);
|
| 125 |
|
|
int use_bufcharge(void);
|
| 126 |
|
|
int use_geom(void);
|
| 127 |
|
|
int use_solv(void);
|
| 128 |
|
|
|
| 129 |
|
|
// ==================================================================
|
| 130 |
|
|
int setup_calculation()
|
| 131 |
|
|
{
|
| 132 |
|
|
int i,j,nRet;
|
| 133 |
|
|
char string[30];
|
| 134 |
|
|
double etot;
|
| 135 |
|
|
|
| 136 |
|
|
potoff(); // turn off all force field terms before resetting
|
| 137 |
|
|
if (minim_control.field == MMFF94)
|
| 138 |
|
|
{
|
| 139 |
|
|
// copy mm3 types into type file and retype
|
| 140 |
|
|
set_field(MMFF94);
|
| 141 |
|
|
set_atomtypes(MMFF94);
|
| 142 |
|
|
if (minim_control.added_const)
|
| 143 |
|
|
get_added_const();
|
| 144 |
|
|
} else
|
| 145 |
|
|
{
|
| 146 |
|
|
if (minim_control.added_const)
|
| 147 |
|
|
{
|
| 148 |
|
|
strcpy(string,"mmxconst.prm");
|
| 149 |
|
|
zero_data();
|
| 150 |
|
|
read_datafiles(string);
|
| 151 |
|
|
get_added_const();
|
| 152 |
|
|
}
|
| 153 |
|
|
type();
|
| 154 |
|
|
set_field(MMX);
|
| 155 |
|
|
}
|
| 156 |
|
|
|
| 157 |
|
|
|
| 158 |
|
|
// allocate memeory for derivatives
|
| 159 |
|
|
get_memory();
|
| 160 |
|
|
|
| 161 |
|
|
// setup bonds, angles, torsions, improper torsions and angles, allenes
|
| 162 |
|
|
get_bonds();
|
| 163 |
|
|
get_angles();
|
| 164 |
|
|
get_torsions();
|
| 165 |
|
|
|
| 166 |
|
|
attach();
|
| 167 |
|
|
// need allene
|
| 168 |
|
|
|
| 169 |
|
|
// set active atoms
|
| 170 |
|
|
set_active();
|
| 171 |
|
|
// setup non_bonded list of atoms to skip
|
| 172 |
|
|
for (i=1; i <= natom; i++)
|
| 173 |
|
|
{
|
| 174 |
|
|
for (j=0; j < MAXIAT; j++)
|
| 175 |
|
|
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9)
|
| 176 |
|
|
{
|
| 177 |
|
|
skip[i][atom.iat[i][j]] = i;
|
| 178 |
|
|
skip[atom.iat[i][j]][i] = atom.iat[i][j];
|
| 179 |
|
|
}
|
| 180 |
|
|
for (j=0; j < attached.n13[i]; j++)
|
| 181 |
|
|
{
|
| 182 |
|
|
skip[i][attached.i13[j][i]] = i;
|
| 183 |
|
|
skip[attached.i13[j][i]][i] = attached.i13[j][i];
|
| 184 |
|
|
}
|
| 185 |
|
|
for(j=0; j < attached.n14[i]; j++)
|
| 186 |
|
|
{
|
| 187 |
|
|
skip[i][attached.i14[j][i]] = -i;
|
| 188 |
|
|
skip[attached.i14[j][i]][i] = -attached.i14[j][i];
|
| 189 |
|
|
}
|
| 190 |
|
|
}
|
| 191 |
|
|
/* assign local geometry potential function parameters */
|
| 192 |
|
|
Missing_constants = FALSE;
|
| 193 |
|
|
if (use_bond() || use_strbnd()) nRet = kbond();
|
| 194 |
|
|
if (nRet == FALSE) // use end_calc to free memory
|
| 195 |
|
|
{
|
| 196 |
|
|
energies.total = 9999.;
|
| 197 |
|
|
return FALSE;
|
| 198 |
|
|
}
|
| 199 |
|
|
if (use_angle() || use_strbnd()) kangle();
|
| 200 |
|
|
if (use_angle() || use_opbend_wilson()) kopbend();
|
| 201 |
|
|
if (use_tors() || use_strtor()) ktorsion();
|
| 202 |
|
|
if (use_strbnd()) kstrbnd();
|
| 203 |
|
|
|
| 204 |
|
|
if (use_hal()) kvdw();
|
| 205 |
|
|
if (use_charge() || use_bufcharge()) kcharge();
|
| 206 |
|
|
if (use_solv()) ksolv();
|
| 207 |
|
|
|
| 208 |
|
|
if (Missing_constants == TRUE)
|
| 209 |
|
|
{
|
| 210 |
|
|
energies.total = 9999.0;
|
| 211 |
|
|
return (FALSE);
|
| 212 |
|
|
}
|
| 213 |
|
|
if (minim_values.iprint == TRUE)
|
| 214 |
|
|
etot = print_energy();
|
| 215 |
|
|
else
|
| 216 |
|
|
etot = energy();
|
| 217 |
|
|
return TRUE;
|
| 218 |
|
|
}
|
| 219 |
|
|
// =================================================================
|
| 220 |
|
|
void end_calculation()
|
| 221 |
|
|
{
|
| 222 |
|
|
|
| 223 |
|
|
free_memory();
|
| 224 |
|
|
}
|
| 225 |
|
|
// ==================================================================
|
| 226 |
|
|
void gradient()
|
| 227 |
|
|
{
|
| 228 |
|
|
int i, j;
|
| 229 |
|
|
|
| 230 |
|
|
energies.estr = 0.0;
|
| 231 |
|
|
energies.ebend = 0.0;
|
| 232 |
|
|
energies.estrbnd = 0.0;
|
| 233 |
|
|
energies.e14 = 0.0;
|
| 234 |
|
|
energies.evdw = 0.0;
|
| 235 |
|
|
energies.etor = 0.0;
|
| 236 |
|
|
energies.eu = 0.0;
|
| 237 |
|
|
energies.eopb = 0.0;
|
| 238 |
|
|
energies.eangang = 0.0;
|
| 239 |
|
|
energies.estrtor = 0.0;
|
| 240 |
|
|
energies.ehbond = 0.0;
|
| 241 |
|
|
energies.efix = 0.0;
|
| 242 |
|
|
energies.eimprop = 0.0;
|
| 243 |
|
|
energies.eimptors = 0.0;
|
| 244 |
|
|
energies.eurey = 0.0;
|
| 245 |
|
|
energies.esolv = 0.0;
|
| 246 |
|
|
energies.egeom =0.0;
|
| 247 |
|
|
|
| 248 |
|
|
for (i=1; i <= natom; i++)
|
| 249 |
|
|
{
|
| 250 |
|
|
for (j=0; j < 3; j++)
|
| 251 |
|
|
{
|
| 252 |
|
|
deriv.deb[i][j] = 0.0;
|
| 253 |
|
|
deriv.dea[i][j] = 0.0;
|
| 254 |
|
|
deriv.destb[i][j] = 0.0;
|
| 255 |
|
|
deriv.deopb[i][j] = 0.0;
|
| 256 |
|
|
deriv.detor[i][j] = 0.0;
|
| 257 |
|
|
deriv.de14[i][j] = 0.0;
|
| 258 |
|
|
deriv.devdw[i][j]= 0.0;
|
| 259 |
|
|
deriv.deqq[i][j] = 0.0;
|
| 260 |
|
|
deriv.deaa[i][j] = 0.0;
|
| 261 |
|
|
deriv.destor[i][j] = 0.0;
|
| 262 |
|
|
deriv.deimprop[i][j] = 0.0;
|
| 263 |
|
|
deriv.dehb[i][j] = 0.0;
|
| 264 |
|
|
deriv.desolv[i][j] = 0.0;
|
| 265 |
|
|
deriv.degeom[i][j] = 0.0;
|
| 266 |
|
|
}
|
| 267 |
|
|
}
|
| 268 |
|
|
|
| 269 |
|
|
if (use_bond())ebond1(natom,bonds_ff.nbnd,bonds_ff.i12,atom.type,atom.tclass,atom.use,atom.x,atom.y,atom.z,bonds_ff.bl,bonds_ff.bk,&energies.estr,deriv.deb);
|
| 270 |
|
|
if (use_angle())eangle1(angles.nang,natom, angles.i13,atom.use,atom.x,atom.y,atom.z,angles.angin,angles.angtype,angles.anat,angles.acon,&energies.ebend,deriv.dea);
|
| 271 |
|
|
if (use_opbend_wilson()) eopbend_wilson1(natom,angles.nang,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.angin,angles.copb,&energies.eopb,deriv.deopb);
|
| 272 |
|
|
if (use_tors())etorsion1(natom,torsions.ntor,torsions.i14,atom.use,atom.x,atom.y,atom.z,torsions.ph1,torsions.ph2,torsions.ph3,torsions.ph4,torsions.ph5,torsions.ph6,
|
| 273 |
|
|
torsions.v1,torsions.v2,torsions.v3,torsions.v4,torsions.v5,torsions.v6,&energies.etor,deriv.detor);
|
| 274 |
|
|
if (use_strbnd())estrbnd1(natom,strbnd.nstrbnd,strbnd.isb,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.anat,bonds_ff.bl,bonds_ff.bk,strbnd.ksb1,strbnd.ksb2,
|
| 275 |
|
|
&energies.estrbnd,deriv.destb);
|
| 276 |
|
|
// mmff
|
| 277 |
|
|
if (use_hal()) ehal1(natom,atom.type,atom.use,atom.x,atom.y,atom.z,cutoffs.vdwcut,skip,nonbond.vrad,nonbond.veps,&energies.evdw,&energies.e14,deriv.devdw,deriv.de14);
|
| 278 |
|
|
if (use_bufcharge()) ebufcharge1(natom,atom.use,skip,atom.x,atom.y,atom.z,atom.charge,cutoffs.chrgcut,&energies.eu,deriv.deqq);
|
| 279 |
|
|
|
| 280 |
|
|
if (use_geom()) egeom1(natom,atom.use,atom.x,atom.y,atom.z,&energies.egeom,deriv.degeom);
|
| 281 |
|
|
if (use_solv()) esolv1(natom,cutoffs.chrgcut,skip,atom.mmx_type,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv,deriv.desolv,deriv.drb);
|
| 282 |
|
|
|
| 283 |
|
|
energies.total = energies.estr + energies.ebend + energies.etor + energies.estrbnd + energies.e14+
|
| 284 |
|
|
energies.evdw + energies.eu + energies.ehbond + energies.eangang + energies.estrtor +
|
| 285 |
|
|
energies.eimprop + energies.eimptors + energies.eopb + energies.eurey + energies.esolv + energies.egeom;
|
| 286 |
|
|
for (i=1; i <= natom; i++)
|
| 287 |
|
|
{
|
| 288 |
|
|
for (j=0; j < 3; j++)
|
| 289 |
|
|
{
|
| 290 |
|
|
deriv.d1[i][j] = deriv.deb[i][j] + deriv.dea[i][j] + deriv.deaa[i][j] +
|
| 291 |
|
|
deriv.destb[i][j] + deriv.detor[i][j] + deriv.deopb[i][j] + deriv.dehb[i][j] +
|
| 292 |
|
|
deriv.destor[i][j] + deriv.deqq[i][j] + deriv.devdw[i][j] + deriv.de14[i][j] +
|
| 293 |
|
|
deriv.deimprop[i][j] + deriv.deub[i][j] + deriv.desolv[i][j] + deriv.degeom[i][j];
|
| 294 |
|
|
|
| 295 |
|
|
}
|
| 296 |
|
|
}
|
| 297 |
|
|
}
|
| 298 |
|
|
// ==================================================================
|
| 299 |
|
|
double get_total_deriv_x(int i)
|
| 300 |
|
|
{
|
| 301 |
|
|
return (deriv.d1[i][0]);
|
| 302 |
|
|
}
|
| 303 |
|
|
double get_total_deriv_y(int i)
|
| 304 |
|
|
{
|
| 305 |
|
|
return (deriv.d1[i][1]);
|
| 306 |
|
|
}
|
| 307 |
|
|
double get_total_deriv_z(int i)
|
| 308 |
|
|
{
|
| 309 |
|
|
return (deriv.d1[i][2]);
|
| 310 |
|
|
}
|
| 311 |
|
|
// ============================================
|
| 312 |
|
|
void print_energy_totals()
|
| 313 |
|
|
{
|
| 314 |
|
|
printf("\nEnergy : %f\n",energies.total);
|
| 315 |
|
|
printf("Str: %f Bnd: %f Tor: %f\n", energies.estr, energies.ebend, energies.etor);
|
| 316 |
|
|
printf("StrBnd: %f VDW: %f QQ: %f\n",energies.estrbnd,energies.evdw+energies.e14+energies.ehbond, energies.eu);
|
| 317 |
|
|
printf("OOP: %f AA: %f Strtor: %f\n",energies.eopb,energies.eangang, energies.estrtor);
|
| 318 |
|
|
if (use_solv()) printf("Solv: %f \n",energies.esolv);
|
| 319 |
|
|
}
|
| 320 |
|
|
// ==================================================================
|
| 321 |
|
|
double get_total_energy()
|
| 322 |
|
|
{
|
| 323 |
|
|
return energies.total;
|
| 324 |
|
|
}
|
| 325 |
|
|
// ==================================================================
|
| 326 |
|
|
double energy()
|
| 327 |
|
|
{
|
| 328 |
|
|
double etot;
|
| 329 |
|
|
int i;
|
| 330 |
|
|
|
| 331 |
|
|
energies.total = 0.0;
|
| 332 |
|
|
energies.estr = 0.0;
|
| 333 |
|
|
energies.ebend = 0.0;
|
| 334 |
|
|
energies.etor = 0.0;
|
| 335 |
|
|
energies.estrbnd = 0.0;
|
| 336 |
|
|
energies.evdw = 0.0;
|
| 337 |
|
|
energies.e14 = 0.0;
|
| 338 |
|
|
energies.ehbond = 0.0;
|
| 339 |
|
|
energies.eu = 0.0;
|
| 340 |
|
|
energies.eangang = 0.0;
|
| 341 |
|
|
energies.estrtor = 0.0;
|
| 342 |
|
|
energies.eimprop = 0.0;
|
| 343 |
|
|
energies.eimptors = 0.0;
|
| 344 |
|
|
energies.eopb = 0.0;
|
| 345 |
|
|
energies.eurey = 0.0;
|
| 346 |
|
|
energies.esolv = 0.0;
|
| 347 |
|
|
energies.egeom = 0.0;
|
| 348 |
|
|
|
| 349 |
|
|
|
| 350 |
|
|
if (use_bond())ebond(bonds_ff.nbnd,bonds_ff.i12,atom.type,atom.tclass,atom.use,atom.x,atom.y,
|
| 351 |
|
|
atom.z,bonds_ff.bl,bonds_ff.bk,&energies.estr);
|
| 352 |
|
|
if (use_angle())eangle(angles.nang,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.angin,angles.angtype,angles.anat,angles.acon,&energies.ebend);
|
| 353 |
|
|
if (use_opbend_wilson()) eopbend_wilson(angles.nang,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.angin,angles.copb,&energies.eopb);
|
| 354 |
|
|
if (use_tors())etorsion(torsions.ntor,torsions.i14,atom.use,atom.type,atom.x,atom.y,atom.z,torsions.ph1,torsions.ph2,torsions.ph3,torsions.ph4,torsions.ph5,
|
| 355 |
|
|
torsions.ph6,torsions.v1,torsions.v2,torsions.v3,torsions.v4,torsions.v5,torsions.v6,&energies.etor);
|
| 356 |
|
|
if (use_strbnd())estrbnd(strbnd.nstrbnd,strbnd.isb,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.anat,bonds_ff.bl,bonds_ff.bk,strbnd.ksb1,strbnd.ksb2,
|
| 357 |
|
|
&energies.estrbnd);
|
| 358 |
|
|
// mmff
|
| 359 |
|
|
if (use_hal()) ehal(natom,atom.type,atom.use,atom.x,atom.y,atom.z,cutoffs.vdwcut,skip,nonbond.vrad,nonbond.veps,&energies.evdw,&energies.e14);
|
| 360 |
|
|
if (use_bufcharge()) ebufcharge(natom,atom.use,skip,atom.x,atom.y,atom.z,atom.charge,cutoffs.chrgcut,&energies.eu);
|
| 361 |
|
|
|
| 362 |
|
|
if (use_geom()) egeom(natom,atom.use,atom.x,atom.y,atom.z,&energies.egeom);
|
| 363 |
|
|
if (use_solv()) esolv(natom,cutoffs.chrgcut,skip,atom.mmx_type,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv);
|
| 364 |
|
|
|
| 365 |
|
|
energies.total = energies.estr + energies.ebend + energies.etor + energies.estrbnd
|
| 366 |
|
|
+ energies.evdw + energies.e14 + energies.ehbond + energies.eu + energies.eangang +
|
| 367 |
|
|
energies.estrtor + energies.eimprop + energies.eimptors + energies.eopb + energies.eurey + energies.esolv + energies.egeom;
|
| 368 |
|
|
etot = energies.total;
|
| 369 |
|
|
return (etot);
|
| 370 |
|
|
}
|
| 371 |
|
|
/* =========================================================================== */
|
| 372 |
|
|
double print_energy()
|
| 373 |
|
|
{
|
| 374 |
|
|
double etot;
|
| 375 |
|
|
int i;
|
| 376 |
|
|
|
| 377 |
|
|
energies.total = 0.0;
|
| 378 |
|
|
energies.estr = 0.0;
|
| 379 |
|
|
energies.ebend = 0.0;
|
| 380 |
|
|
energies.etor = 0.0;
|
| 381 |
|
|
energies.estrbnd = 0.0;
|
| 382 |
|
|
energies.evdw = 0.0;
|
| 383 |
|
|
energies.e14 = 0.0;
|
| 384 |
|
|
energies.ehbond = 0.0;
|
| 385 |
|
|
energies.eu = 0.0;
|
| 386 |
|
|
energies.eangang = 0.0;
|
| 387 |
|
|
energies.estrtor = 0.0;
|
| 388 |
|
|
energies.eimprop = 0.0;
|
| 389 |
|
|
energies.eimptors = 0.0;
|
| 390 |
|
|
energies.eopb = 0.0;
|
| 391 |
|
|
energies.eurey = 0.0;
|
| 392 |
|
|
energies.esolv = 0.0;
|
| 393 |
|
|
energies.egeom = 0.0;
|
| 394 |
|
|
|
| 395 |
|
|
|
| 396 |
|
|
if (use_bond())ebond(bonds_ff.nbnd,bonds_ff.i12,atom.type,atom.tclass,atom.use,atom.x,atom.y,
|
| 397 |
|
|
atom.z,bonds_ff.bl,bonds_ff.bk,&energies.estr);
|
| 398 |
|
|
if (use_angle())eangle(angles.nang,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.angin,angles.angtype,angles.anat,angles.acon,&energies.ebend);
|
| 399 |
|
|
if (use_opbend_wilson()) eopbend_wilson(angles.nang,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.angin,angles.copb,&energies.eopb);
|
| 400 |
|
|
if (use_tors())etorsion(torsions.ntor,torsions.i14,atom.use,atom.type,atom.x,atom.y,atom.z,torsions.ph1,torsions.ph2,torsions.ph3,torsions.ph4,torsions.ph5,
|
| 401 |
|
|
torsions.ph6,torsions.v1,torsions.v2,torsions.v3,torsions.v4,torsions.v5,torsions.v6,&energies.etor);
|
| 402 |
|
|
if (use_strbnd())estrbnd(strbnd.nstrbnd,strbnd.isb,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.anat,bonds_ff.bl,bonds_ff.bk,strbnd.ksb1,strbnd.ksb2,
|
| 403 |
|
|
&energies.estrbnd);
|
| 404 |
|
|
// mmff
|
| 405 |
|
|
if (use_hal()) ehal(natom,atom.type,atom.use,atom.x,atom.y,atom.z,cutoffs.vdwcut,skip,nonbond.vrad,nonbond.veps,&energies.evdw,&energies.e14);
|
| 406 |
|
|
if (use_bufcharge()) ebufcharge(natom,atom.use,skip,atom.x,atom.y,atom.z,atom.charge,cutoffs.chrgcut,&energies.eu);
|
| 407 |
|
|
|
| 408 |
|
|
if (use_geom()) egeom(natom,atom.use,atom.x,atom.y,atom.z,&energies.egeom);
|
| 409 |
|
|
if (use_solv()) esolv(natom,cutoffs.chrgcut,skip,atom.mmx_type,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv);
|
| 410 |
|
|
|
| 411 |
|
|
energies.total = energies.estr + energies.ebend + energies.etor + energies.estrbnd
|
| 412 |
|
|
+ energies.evdw + energies.e14 + energies.ehbond + energies.eu + energies.eangang +
|
| 413 |
|
|
energies.estrtor + energies.eimprop + energies.eimptors + energies.eopb + energies.eurey + energies.esolv + energies.egeom;
|
| 414 |
|
|
etot = energies.total;
|
| 415 |
|
|
|
| 416 |
|
|
return (etot);
|
| 417 |
|
|
}
|
| 418 |
|
|
// ====================== hessian =======================
|
| 419 |
|
|
void hessian(int maxhess, double *h, int *hinit, int *hstop,int *hindex, double *hdiag)
|
| 420 |
|
|
{
|
| 421 |
|
|
int i,j,k,nhess;
|
| 422 |
|
|
double hmax;
|
| 423 |
|
|
char hatext[60];
|
| 424 |
|
|
|
| 425 |
|
|
int *keep; // keep[MAXATOM];
|
| 426 |
|
|
|
| 427 |
|
|
keep = ivector(0,natom);
|
| 428 |
|
|
|
| 429 |
|
|
nhess = 0;
|
| 430 |
|
|
for (i=1; i <= natom; i++)
|
| 431 |
|
|
{
|
| 432 |
|
|
|
| 433 |
|
|
hinit[nhess] = 0;
|
| 434 |
|
|
hstop[nhess] = 0;
|
| 435 |
|
|
hdiag[nhess] = 0.0;
|
| 436 |
|
|
nhess++;
|
| 437 |
|
|
hinit[nhess] = 0;
|
| 438 |
|
|
hstop[nhess] = 0;
|
| 439 |
|
|
hdiag[nhess] = 0.0;
|
| 440 |
|
|
nhess++;
|
| 441 |
|
|
hinit[nhess] = 0;
|
| 442 |
|
|
hstop[nhess] = 0;
|
| 443 |
|
|
hdiag[nhess] = 0.0;
|
| 444 |
|
|
nhess++;
|
| 445 |
|
|
}
|
| 446 |
|
|
/* periodic boundary conditions set here */
|
| 447 |
|
|
|
| 448 |
|
|
// if (use_picalc) piseq(0,0);
|
| 449 |
|
|
|
| 450 |
|
|
nhess= 0;
|
| 451 |
|
|
for (i=1; i <= natom; i++)
|
| 452 |
|
|
{
|
| 453 |
|
|
for(k=1; k <= natom; k++)
|
| 454 |
|
|
{
|
| 455 |
|
|
for(j=0; j < 3; j++)
|
| 456 |
|
|
{
|
| 457 |
|
|
hess.hessx[k][j] = 0.0;
|
| 458 |
|
|
hess.hessy[k][j] = 0.0;
|
| 459 |
|
|
hess.hessz[k][j] = 0.0;
|
| 460 |
|
|
}
|
| 461 |
|
|
}
|
| 462 |
|
|
|
| 463 |
|
|
if (atom.use[i])
|
| 464 |
|
|
{
|
| 465 |
|
|
if (use_bond())ebond2(i,bonds_ff.i12,atom.iat,atom.bo,atom.x,atom.y,atom.z,bonds_ff.bl,bonds_ff.bk,hess.hessx,hess.hessy,hess.hessz);
|
| 466 |
|
|
if (use_angle())eangle2(i,angles.nang,angles.i13,angles.angin,atom.x,atom.y,atom.z,angles.acon,angles.anat,deriv.dea,hess.hessx,hess.hessy,hess.hessz);
|
| 467 |
|
|
if (use_strbnd())estrbnd2(i,strbnd.nstrbnd,strbnd.isb,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.anat,bonds_ff.bl,bonds_ff.bk,strbnd.ksb1,strbnd.ksb2,
|
| 468 |
|
|
hess.hessx,hess.hessy,hess.hessz);
|
| 469 |
|
|
if (use_opbend_wilson()) eopbend_wilson2(i,angles.nang,angles.i13,atom.use,atom.x,atom.y,atom.z,angles.angin,angles.copb,hess.hessx,hess.hessy,hess.hessz);
|
| 470 |
|
|
if (use_tors())etorsion2(i,torsions.ntor,torsions.i14,atom.use,atom.x,atom.y,atom.z,torsions.ph1,torsions.ph2,torsions.ph3,torsions.ph4,torsions.ph5,
|
| 471 |
|
|
torsions.ph6,torsions.v1,torsions.v2,torsions.v3,torsions.v4,torsions.v5,torsions.v6,hess.hessx,hess.hessy,hess.hessz);
|
| 472 |
|
|
|
| 473 |
|
|
if (use_hal())ehal2(i,natom,atom.type,atom.use,atom.x,atom.y,atom.z,cutoffs.vdwcut,skip,nonbond.vrad,nonbond.veps,hess.hessx,hess.hessy,hess.hessz);
|
| 474 |
|
|
if (use_bufcharge())ebufcharge2(i,natom,atom.use,skip,atom.x,atom.y,atom.z,atom.charge,cutoffs.chrgcut,hess.hessx,hess.hessy,hess.hessz);
|
| 475 |
|
|
|
| 476 |
|
|
if (use_geom()) egeom2(i,natom,atom.use,atom.x,atom.y,atom.z,hess.hessx,hess.hessy,hess.hessz);
|
| 477 |
|
|
if (use_solv()) esolv2(i,natom,cutoffs.chrgcut,atom.mmx_type,atom.charge,atom.x,atom.y,atom.z,hess.hessx,hess.hessy,hess.hessz);
|
| 478 |
|
|
|
| 479 |
|
|
hdiag[(i-1)*3] += hess.hessx[i][0];
|
| 480 |
|
|
hdiag[(i-1)*3+1] += hess.hessy[i][1];
|
| 481 |
|
|
hdiag[(i-1)*3+2] += hess.hessz[i][2];
|
| 482 |
|
|
|
| 483 |
|
|
for (k=i+1; k <= natom; k++)
|
| 484 |
|
|
{
|
| 485 |
|
|
keep[k] = FALSE;
|
| 486 |
|
|
if (atom.use[k])
|
| 487 |
|
|
{
|
| 488 |
|
|
hmax = fabs(hess.hessx[k][0]);
|
| 489 |
|
|
for (j=0; j < 3;j++)
|
| 490 |
|
|
{
|
| 491 |
|
|
if (fabs(hess.hessx[k][j]) > hmax)
|
| 492 |
|
|
hmax = fabs(hess.hessx[k][j]);
|
| 493 |
|
|
}
|
| 494 |
|
|
for (j=0; j < 3;j++)
|
| 495 |
|
|
{
|
| 496 |
|
|
if (fabs(hess.hessy[k][j]) > hmax)
|
| 497 |
|
|
hmax = fabs(hess.hessy[k][j]);
|
| 498 |
|
|
}
|
| 499 |
|
|
for (j=0; j < 3;j++)
|
| 500 |
|
|
{
|
| 501 |
|
|
if (fabs(hess.hessz[k][j]) > hmax)
|
| 502 |
|
|
hmax = fabs(hess.hessz[k][j]);
|
| 503 |
|
|
}
|
| 504 |
|
|
if (hmax >= hesscut) keep[k] = TRUE;
|
| 505 |
|
|
}
|
| 506 |
|
|
}
|
| 507 |
|
|
|
| 508 |
|
|
hinit[(i-1)*3] = nhess; // x component of new atom
|
| 509 |
|
|
|
| 510 |
|
|
hindex[nhess] = 3*(i-1) + 1;
|
| 511 |
|
|
h[nhess] = hess.hessx[i][1];
|
| 512 |
|
|
nhess++;
|
| 513 |
|
|
hindex[nhess] = 3*(i-1) + 2;
|
| 514 |
|
|
h[nhess] = hess.hessx[i][2];
|
| 515 |
|
|
nhess++;
|
| 516 |
|
|
|
| 517 |
|
|
for (k=i+1; k <= natom; k++)
|
| 518 |
|
|
{
|
| 519 |
|
|
if (keep[k])
|
| 520 |
|
|
{
|
| 521 |
|
|
for (j=0; j < 3; j++)
|
| 522 |
|
|
{
|
| 523 |
|
|
hindex[nhess] = 3*(k-1) +j;
|
| 524 |
|
|
h[nhess] = hess.hessx[k][j];
|
| 525 |
|
|
nhess++;
|
| 526 |
|
|
}
|
| 527 |
|
|
}
|
| 528 |
|
|
}
|
| 529 |
|
|
hstop[(i-1)*3] = nhess;
|
| 530 |
|
|
|
| 531 |
|
|
hinit[(i-1)*3+1] = nhess; // y component of atom i
|
| 532 |
|
|
hindex[nhess] = 3*(i-1) + 2;
|
| 533 |
|
|
h[nhess] = hess.hessy[i][2];
|
| 534 |
|
|
nhess++;
|
| 535 |
|
|
for (k=i+1; k <= natom; k++)
|
| 536 |
|
|
{
|
| 537 |
|
|
if (keep[k])
|
| 538 |
|
|
{
|
| 539 |
|
|
for (j=0; j < 3; j++)
|
| 540 |
|
|
{
|
| 541 |
|
|
hindex[nhess] = 3*(k-1) +j;
|
| 542 |
|
|
h[nhess] = hess.hessy[k][j];
|
| 543 |
|
|
nhess++;
|
| 544 |
|
|
}
|
| 545 |
|
|
}
|
| 546 |
|
|
}
|
| 547 |
|
|
hstop[(i-1)*3+1] = nhess;
|
| 548 |
|
|
hinit[(i-1)*3+2] = nhess;
|
| 549 |
|
|
for (k=i+1; k <= natom; k++)
|
| 550 |
|
|
{
|
| 551 |
|
|
if (keep[k])
|
| 552 |
|
|
{
|
| 553 |
|
|
for (j=0; j < 3; j++)
|
| 554 |
|
|
{
|
| 555 |
|
|
hindex[nhess] = 3*(k-1) +j;
|
| 556 |
|
|
h[nhess] = hess.hessz[k][j];
|
| 557 |
|
|
nhess++;
|
| 558 |
|
|
}
|
| 559 |
|
|
}
|
| 560 |
|
|
}
|
| 561 |
|
|
hstop[(i-1)*3+2] = nhess;
|
| 562 |
|
|
|
| 563 |
|
|
if (nhess > maxhess)
|
| 564 |
|
|
{
|
| 565 |
|
|
sprintf(hatext,"Too many hessian elements: %d elements %d max\n",nhess,maxhess);
|
| 566 |
|
|
message_alert(hatext,"Error");
|
| 567 |
|
|
fprintf(pcmlogfile,"Too many hessian elements !\n");
|
| 568 |
|
|
strcpy(Openbox.fname,"Hesserr.pcm");
|
| 569 |
|
|
exit(0);
|
| 570 |
|
|
}
|
| 571 |
|
|
}
|
| 572 |
|
|
}
|
| 573 |
|
|
free_ivector(keep, 0,natom);
|
| 574 |
|
|
}
|
| 575 |
|
|
|
