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#include "cutoffs.h" |
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#include "nonbond.h" |
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#include "torsions.h" |
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+ |
#include "fix.h" |
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EXTERN struct t_strbnd { |
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int nstrbnd, **isb; |
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void attach(void); |
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void get_bonds(void); |
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void get_angles(void); |
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< |
void get_torsions(void); |
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> |
void get_torsions(int natom,int *type,int **iat,int **bo); |
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void set_field(int); |
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double energy(void); |
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double get_total_energy(void); |
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double get_total_deriv_y(int i); |
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double get_total_deriv_z(int i); |
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double print_energy(void); |
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< |
void set_active(void); |
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> |
void set_active(int natom,int *use,int natom_fix,int *katm_fix); |
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int setup_calculation(void); |
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void end_calculation(void); |
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|
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float *ksb2,double *estrbnd,double **destb); |
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void egeom(int natom,int *use,double *x,double *y,double *z,double *egeom); |
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void egeom1(int natom,int *use,double *x,double *y,double *z,double *egeom,double **degeom); |
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< |
void esolv(int natom,double chrgcut,int **skip,int *mmx_type,int *use,double *charge,double *x,double *y,double *z,double *esolv); |
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< |
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); |
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> |
void esolv(int natom,double chrgcut,int **skip,int *use,double *charge,double *x,double *y,double *z,double *esolv); |
| 82 |
> |
void esolv1(int natom,double chrgcut,int **skip,int *use,double *charge,double *x,double *y,double *z,double *esolv,double **desolv,double *drb); |
| 83 |
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| 84 |
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void hessian(int, double *,int *, int *, int *,double *); |
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void ebond2(int ia,int **,int **,int **,double *x,double *y,double *z,double *bl,double *bk,float **hessx,float **hessy,float **hessz); |
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float **hessx,float **hessy,float **hessz); |
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void estrbnd2(int iatom,int nstrbnd,int **,int **,int *use,double *x,double *y,double *z,float *anat,double *bl,double *bk,float *ksb1, |
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float *ksb2,float **hessx,float **hessy,float **hessz); |
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< |
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 esolv2(int ia,int natom,double chrgcut,double *charge,double *x,double *y,double *z,float **hessx,float **hessy,float **hessz); |
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void egeom2(int ,int natom,int *use,double *x,double *y,double *z,float **hessx,float **hessy,float **hessz); |
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| 99 |
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void kangle(void); |
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// setup bonds, angles, torsions, improper torsions and angles, allenes |
| 163 |
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get_bonds(); |
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get_angles(); |
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< |
get_torsions(); |
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> |
get_torsions(natom,atom.type,atom.iat,atom.bo); |
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| 167 |
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attach(); |
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// need allene |
| 169 |
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| 170 |
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// set active atoms |
| 171 |
< |
set_active(); |
| 171 |
> |
set_active(natom,atom.use,fx_atom.natom_fix,fx_atom.katom_fix); |
| 172 |
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// setup non_bonded list of atoms to skip |
| 173 |
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for (i=1; i <= natom; i++) |
| 174 |
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{ |
| 279 |
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if (use_bufcharge()) ebufcharge1(natom,atom.use,skip,atom.x,atom.y,atom.z,atom.charge,cutoffs.chrgcut,&energies.eu,deriv.deqq); |
| 280 |
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|
| 281 |
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if (use_geom()) egeom1(natom,atom.use,atom.x,atom.y,atom.z,&energies.egeom,deriv.degeom); |
| 282 |
< |
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 |
> |
if (use_solv()) esolv1(natom,cutoffs.chrgcut,skip,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv,deriv.desolv,deriv.drb); |
| 283 |
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|
| 284 |
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energies.total = energies.estr + energies.ebend + energies.etor + energies.estrbnd + energies.e14+ |
| 285 |
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energies.evdw + energies.eu + energies.ehbond + energies.eangang + energies.estrtor + |
| 361 |
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if (use_bufcharge()) ebufcharge(natom,atom.use,skip,atom.x,atom.y,atom.z,atom.charge,cutoffs.chrgcut,&energies.eu); |
| 362 |
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|
| 363 |
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if (use_geom()) egeom(natom,atom.use,atom.x,atom.y,atom.z,&energies.egeom); |
| 364 |
< |
if (use_solv()) esolv(natom,cutoffs.chrgcut,skip,atom.mmx_type,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv); |
| 364 |
> |
if (use_solv()) esolv(natom,cutoffs.chrgcut,skip,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv); |
| 365 |
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|
| 366 |
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energies.total = energies.estr + energies.ebend + energies.etor + energies.estrbnd |
| 367 |
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+ energies.evdw + energies.e14 + energies.ehbond + energies.eu + energies.eangang + |
| 407 |
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if (use_bufcharge()) ebufcharge(natom,atom.use,skip,atom.x,atom.y,atom.z,atom.charge,cutoffs.chrgcut,&energies.eu); |
| 408 |
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|
| 409 |
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if (use_geom()) egeom(natom,atom.use,atom.x,atom.y,atom.z,&energies.egeom); |
| 410 |
< |
if (use_solv()) esolv(natom,cutoffs.chrgcut,skip,atom.mmx_type,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv); |
| 410 |
> |
if (use_solv()) esolv(natom,cutoffs.chrgcut,skip,atom.use,atom.charge,atom.x,atom.y,atom.z,&energies.esolv); |
| 411 |
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|
| 412 |
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energies.total = energies.estr + energies.ebend + energies.etor + energies.estrbnd |
| 413 |
|
+ energies.evdw + energies.e14 + energies.ehbond + energies.eu + energies.eangang + |
| 475 |
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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); |
| 476 |
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|
| 477 |
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if (use_geom()) egeom2(i,natom,atom.use,atom.x,atom.y,atom.z,hess.hessx,hess.hessy,hess.hessz); |
| 478 |
< |
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 |
> |
if (use_solv()) esolv2(i,natom,cutoffs.chrgcut,atom.charge,atom.x,atom.y,atom.z,hess.hessx,hess.hessy,hess.hessz); |
| 479 |
|
|
| 480 |
|
hdiag[(i-1)*3] += hess.hessx[i][0]; |
| 481 |
|
hdiag[(i-1)*3+1] += hess.hessy[i][1]; |
