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align.cpp
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// Please see license.txt for licensing and copyright information //
// Author: Paul Zimmerman, University of Michigan //
#include "align.h"
using namespace std;
//to do
// implement point out for planes
double norm(double* x, int size)
{
double val = 0.;
for (int i=0;i<size;i++)
val += x[i]*x[i];
val = sqrt(val);
return val;
}
void Align::shuttle_align(int nadd1, int* add1)
{
if (inited!=3)
{
printf(" in shuttle_align, add_third hasn't been called \n");
exit(1);
}
#if 0
printf("\n in shuttle_align, adding:");
for (int i=0;i<nadd1;i++)
printf(" %i-%i",add1[2*i+0]+1,add1[2*i+1]+1);
printf("\n");
//printf(" in shuttle_align natoms1: %i natoms2: %i \n",natoms1,natoms2);
#endif
#if 0
printf(" previous geom: \n");
print_xyz();
#endif
int na12 = natoms1 + natoms2;
///get v1's for all add atoms
double* v1a = new double[3*nadd1];
for (int i=0;i<3*nadd1;i++) v1a[i] = 0.;
double* v1b = new double[3*nadd1];
for (int i=0;i<3*nadd1;i++) v1b[i] = 0.;
double* c1 = new double[6]; //center points
string* anames12 = new string[na12+1];
int* anumbers12 = new int[na12+1];
for (int i=0;i<natoms1;i++)
anames12[i] = anames1[i];
for (int i=0;i<natoms2;i++)
anames12[natoms1+i] = anames2[i];
for (int i=0;i<natoms1;i++)
anumbers12[i] = anumbers1[i];
for (int i=0;i<natoms2;i++)
anumbers12[natoms1+i] = anumbers2[i];
int* bonded1 = new int[8];
int* bonded2 = new int[8];
int* bonded3 = new int[8];
ICoord ic1,ic2;
ic1.init(na12,anames12,anumbers12,xyza);
ic1.make_frags();
ic1.bond_frags();
//ic1.ic_create_nobonds();
ic2.init(natoms3,anames3,anumbers3,xyz3);
ic2.make_frags();
ic2.bond_frags();
//ic2.ic_create_nobonds();
int npf1 = 0;
int npf2 = 0;
int nvf1 = 0;
int nvf2 = 0;
int found = 0;
for (int i=0;i<nadd1;i++)
{
int a1 = add1[2*i+0];
int a2 = add1[2*i+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
int same_frag = check_frag_3(a1,a2);
//printf(" a1: %i a2: %i same_frag: %i \n",a1+1,a2+1,same_frag);
a2 -= na12;
if (!same_frag)
{
found = 1;
int nbondsa1, nbondsa2;
nbondsa1 = get_bonds(a1,ic1,bonded1);
nbondsa2 = get_bonds(a2,ic2,bonded2);
//first atom's vector
for (int j=0;j<nbondsa1;j++)
{
v1a[3*nvf1+0] += xyza[3*a1+0] - xyza[3*bonded1[j]+0];
v1a[3*nvf1+1] += xyza[3*a1+1] - xyza[3*bonded1[j]+1];
v1a[3*nvf1+2] += xyza[3*a1+2] - xyza[3*bonded1[j]+2];
}
if (nbondsa1==2)
{
double anglev = ic1.angle_val(bonded1[0],a1,bonded1[1]);
if (anglev>175.)
{
//printf(" using ool v1 \n");
linear_right(&v1a[3*nvf1],a1,bonded1,xyza);
}
}
if (nbondsa1==3)
{
double imptorv = ic1.torsion_val(bonded1[0],a1,bonded1[1],bonded1[2]);
//printf(" imptorv: %4.2f \n",imptorv);
if (fabs(imptorv)>175.)
{
//printf(" using oop v1 \n");
planar_cross(&v1a[3*nvf1],a1,bonded1,xyza);
npf1++;
}
}
if (npf1>1)
{
align_v1(nvf1+1,v1a);
}
double n1 = norm(&v1a[3*nvf1],3);
for (int j=0;j<3;j++)
v1a[3*nvf1+j] = v1a[3*nvf1+j] / n1;
#if 0
printf(" v1a(a1): \n");
for (int j=0;j<3;j++)
printf(" %4.3f",v1a[3*nvf1+j]);
printf("\n");
#endif
nvf1++;
//second atom's vector
for (int j=0;j<nbondsa2;j++)
{
v1b[3*nvf2+0] += xyz3[3*a2+0] - xyz3[3*bonded2[j]+0];
v1b[3*nvf2+1] += xyz3[3*a2+1] - xyz3[3*bonded2[j]+1];
v1b[3*nvf2+2] += xyz3[3*a2+2] - xyz3[3*bonded2[j]+2];
}
if (nbondsa2==2)
{
double anglev = ic2.angle_val(bonded2[0],a2,bonded2[1]);
if (anglev>175.)
{
//printf(" using ool v1 (linear angle found) \n");
linear_right(&v1b[3*nvf2],a2,bonded2,xyz3);
}
}
if (nbondsa2==3)
{
double imptorv = ic2.torsion_val(bonded2[0],a2,bonded2[1],bonded2[2]);
//printf(" imptorv: %4.2f \n",imptorv);
if (fabs(imptorv)>175.)
{
//printf(" using oop v1 (planar atom found) \n");
planar_cross(&v1b[3*nvf2],a2,bonded2,xyz3);
npf2++;
}
}
if (npf2>1)
{
align_v1(nvf2+1,v1b);
}
n1 = norm(&v1b[3*nvf2],3);
for (int j=0;j<3;j++)
v1b[3*nvf2+j] = v1b[3*nvf2+j] / n1;
#if 0
printf(" v1b(a2): \n");
for (int j=0;j<3;j++)
printf(" %4.3f",v1b[3*nvf2+j]);
printf("\n");
#endif
nvf2++;
} // if !same_frag
} //loop i over nadd
if (!found)
{
//printf(" couldn't find anything to align \n");
return;
}
#if 0
//CPMZ NOT IMPLEMENTED
if (npf1>0)
point_out(v1a,natoms1,xyz1);
if (npf2>0)
point_out(v1b,natoms2,xyz2);
#endif
//averaging over v1 to get v2
double* v2 = new double[6];
for (int i=0;i<6;i++) v2[i] = 0.;
for (int i=0;i<nadd1;i++)
{
for (int j=0;j<3;j++)
v2[j] += v1a[3*i+j];
for (int j=0;j<3;j++)
v2[3+j] += v1b[3*i+j];
}
double n1 = norm(v2,3);
double n2 = norm(&v2[3],3);
if (n1<0.000001)
{
int a1 = add1[2*(nadd1-1)+0];
int a2 = add1[2*(nadd1-1)+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
int nbondsa1 = get_bonds(a1,ic1,bonded1);
linear_right(v2,a1,bonded1,xyza);
n1 = norm(v2,3);
// printf(" new norm: %8.6f \n",n1);
}
if (n2<0.000001)
{
int a1 = add1[2*(nadd1-1)+0];
int a2 = add1[2*(nadd1-1)+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
a2 -= na12;
int nbondsa2 = get_bonds(a2,ic2,bonded2);
linear_right(&v2[3],a2,bonded2,xyz3);
n2 = norm(&v2[3],3);
// printf(" new norm: %8.6f \n",n2);
}
for (int i=0;i<3;i++)
v2[i] = v2[i] / n1;
for (int i=3;i<6;i++)
v2[i] = v2[i] / n2;
#if 0
printf(" v2(1):");
for (int j=0;j<3;j++)
printf(" %4.3f",v2[j]);
printf("\n");
printf(" v2(2):");
for (int j=0;j<3;j++)
printf(" %4.3f",v2[3+j]);
printf("\n");
#endif
//get central location for each
int cfound = 0;
for (int i=0;i<6;i++) c1[i] = 0.;
for (int i=0;i<nadd1;i++)
{
int a1 = add1[2*i+0];
int a2 = add1[2*i+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
int same_frag = check_frag_3(a1,a2);
a2 -= na12;
if (!same_frag)
{
//printf(" c1 for %i-%i \n",a1+1,a2+1);
cfound++;
for (int j=0;j<3;j++)
c1[j] += xyza[3*a1+j];
for (int j=0;j<3;j++)
c1[3+j] += xyz3[3*a2+j];
}
} //loop i over nadd
if (cfound>1)
for (int j=0;j<6;j++)
c1[j] = c1[j] / cfound;
#if 0
printf(" c1:");
for (int j=0;j<6;j++)
printf(" %4.3f",c1[j]);
printf("\n");
#endif
//move geometry to center
double* xyz12a = new double[3*(na12+2)];
double* xyz3a = new double[3*(natoms3+2)];
string* anames12a = new string[na12+2];
string* anames3a = new string[natoms3+2];
for (int i=0;i<natoms1;i++) anames12a[i] = anames1[i];
for (int i=0;i<natoms2;i++) anames12a[natoms1+i] = anames2[i];
anames12a[na12] = "X";
anames12a[na12+1] = "X";
for (int i=0;i<natoms3;i++) anames3a[i] = anames3[i];
anames3a[natoms3] = "X";
anames3a[natoms3+1] = "X";
for (int i=0;i<natoms1;i++)
{
for (int j=0;j<3;j++)
xyz12a[3*i+j] = xyz1[3*i+j] - c1[j];
}
for (int i=0;i<natoms2;i++)
{
for (int j=0;j<3;j++)
xyz12a[3*natoms1+3*i+j] = xyz2[3*i+j] - c1[j];
}
xyz12a[3*(na12)+0] = 0.; xyz12a[3*(na12)+1] = 0.;
xyz12a[3*(na12)+2] = 0.; xyz12a[3*(na12+1)+0] = v2[0];
xyz12a[3*(na12+1)+1] = v2[1]; xyz12a[3*(na12+1)+2] = v2[2];
//print_xyz_gen(na12+2,anames12a,xyz12a);
for (int i=0;i<natoms3;i++)
{
for (int j=0;j<3;j++)
xyz3a[3*i+j] = xyz3[3*i+j] - c1[3+j];
}
xyz3a[3*(natoms3)+0] = 0.; xyz3a[3*(natoms3)+1] = 0.;
xyz3a[3*(natoms3)+2] = 0.; xyz3a[3*(natoms3+1)+0] = v2[3];
xyz3a[3*(natoms3+1)+1] = v2[4]; xyz3a[3*(natoms3+1)+2] = v2[5];
//print_xyz_gen(natoms3+2,anames3a,xyz3a);
//align v2 along x/-x direction
int t1 = na12;
int t2 = na12+1;
align_to_x(na12+2,t1,t2,xyz12a,anames12a,1,10.);
t1 = natoms3;
t2 = natoms3+1;
align_to_x(natoms3+2,t1,t2,xyz3a,anames3a,-1,10.);
//print_xyz_gen(na12+2,anames12a,xyz12a);
//print_xyz_gen(natoms3+2,anames3a,xyz3a);
//face each other at X Angstroms
double X = 8.;
for (int i=0;i<3*natoms1;i++)
xyz1[i] = xyz12a[i];
for (int i=0;i<3*natoms2;i++)
xyz2[i] = xyz12a[3*natoms1+i];
for (int i=0;i<3*natoms3;i++)
xyz3[i] = xyz3a[i];
for (int i=0;i<natoms3;i++)
xyz3[3*i+0] += X;
//prepare for vdw opt
string* anamesp = new string[na12+natoms3];
int* anumbersp = new int[na12+natoms3];
for (int i=0;i<natoms1;i++)
anamesp[i] = anames1[i];
for (int i=0;i<natoms2;i++)
anamesp[natoms1+i] = anames2[i];
for (int i=0;i<natoms3;i++)
anamesp[na12+i] = anames3[i];
for (int i=0;i<natoms1;i++)
anumbersp[i] = anumbers1[i];
for (int i=0;i<natoms2;i++)
anumbersp[natoms1+i] = anumbers2[i];
for (int i=0;i<natoms3;i++)
anumbersp[na12+i] = anumbers3[i];
//full pair geometry, before vdw opt
for (int i=0;i<3*natoms1;i++)
xyza3[i] = xyz1[i];
for (int i=0;i<3*natoms2;i++)
xyza3[3*natoms1+i] = xyz2[i];
for (int i=0;i<3*natoms3;i++)
xyza3[3*(na12)+i] = xyz3[i];
ICoord icp;
icp.init(na12+natoms3,anamesp,anumbersp,xyza3);
//print_xyz();
//rotate about central axis
if (nadd1>1)
{
int a1 = add1[0];
int a2 = add1[1];
int tmp1 = a1; if (a1>a2) { a1 = a2; a2 = tmp1; }
int a3 = add1[2];
int a4 = add1[3];
int tmp2 = a3; if (a3>a4) { a3 = a4; a4 = tmp2; }
int same_frag = check_frag_3(a1,a2) + check_frag_3(a3,a4);
if (!same_frag && a1!=a3 && a2!=a4)
{
double torv = icp.torsion_val(a1,a3,a4,a2);
//printf(" central torv: %4.2f (%i %i %i %i) \n",torv,a1+1,a3+1,a4+1,a2+1);
rotate_around_x(na12,natoms3,-torv,icp.coords);
}
}
double* vx = new double[3];
vx[1] = vx[2] = 0.;
vx[0] = 1.0;
vdw_vector_opt(na12,natoms3,vx,icp);
delete [] vx;
for (int i=0;i<3*(na12+natoms3);i++)
xyza3[i] = icp.coords[i];
for (int i=0;i<3*natoms1;i++)
xyz1[i] = xyza3[i];
for (int i=0;i<3*natoms2;i++)
xyz2[i] = xyza3[3*natoms1+i];
for (int i=0;i<3*natoms3;i++)
xyz3[i] = xyza3[3*(na12)+i];
//print_xyz_gen(na12,icp.anames,xyza);
int badgeom = 0;
for (int i=0;i<3*natoms1;i++)
if (xyz1[i]!=xyz1[i])
{
badgeom = 1;
break;
}
for (int i=0;i<3*natoms2;i++)
if (xyz2[i]!=xyz2[i])
{
badgeom = 1;
break;
}
for (int i=0;i<3*natoms3;i++)
if (xyz3[i]!=xyz3[i])
{
badgeom = 1;
break;
}
if (badgeom)
{
printf(" ERROR: nan detected in shuttle_align, exiting! \n");
print_xyz_gen(natoms1,anames1,xyz1);
print_xyz_gen(natoms2,anames2,xyz2);
print_xyz_gen(natoms3,anames3,xyz3);
exit(1);
}
delete [] anames12;
delete [] anumbers12;
delete [] anames12a;
delete [] anames3a;
delete [] xyz12a;
delete [] xyz3a;
delete [] v2;
delete [] v1a;
delete [] v1b;
delete [] bonded1;
delete [] bonded2;
delete [] bonded3;
ic1.freemem();
ic2.freemem();
delete [] anamesp;
delete [] anumbersp;
icp.freemem();
return;
}
void Align::add_third(int natoms3i, string* anames3i, int* anumbers3i, double* xyz3i)
{
if (!inited)
{
printf(" WARNING: cannot add_third without initing first \n");
return;
}
if (inited==3)
{
if (anames3!=NULL) delete [] anames3;
if (anumbers3!=NULL) delete [] anumbers3;
if (xyz3!=NULL) delete [] xyz3;
if (xyza3!=NULL) delete [] xyza3;
}
inited = 3;
natoms3 = natoms3i;
anames3 = new string[natoms3];
anumbers3 = new int[natoms3];
xyz3 = new double[3*natoms3];
xyza3 = new double[3*(natoms1+natoms2+natoms3)];
for (int i=0;i<natoms3;i++)
{
anames3[i] = anames3i[i];
anumbers3[i] = anumbers3i[i];
}
for (int i=0;i<3*natoms3;i++)
xyz3[i] = xyz3i[i];
return;
}
void Align::vdw_vector_opt(int natoms1, int natoms2, double* v1, ICoord icp)
{
//printf(" in vdw_vector_opt \n");
double E = 0.;
double pE = 0.;
double THRESH = 0.001;
double emin = 1000000.;
for (int i=0;i<200;i++)
{
pE = E;
E = icp.mm_energy();
//printf(" E: %6.5f \n",E);
if (E<emin) emin = E;
if (E>pE+THRESH && E>emin) break;
for (int j=0;j<natoms2;j++)
for (int k=0;k<3;k++)
icp.coords[3*natoms1+3*j+k] -= 0.1*v1[k];
// print_xyz_gen(icp.natoms,icp.anames,icp.coords);
}
return;
}
void Align::point_out(double* v1, int natoms, double* xyz)
{
return;
}
void Align::align_zero()
{
if (inited==0) return;
//printf(" in align_zero \n");
//get vector pointed along COM's
//move close
//full pair geometry
for (int i=0;i<3*natoms1;i++)
xyza[i] = xyz1[i];
for (int i=0;i<3*natoms2;i++)
xyza[3*natoms1+i] = xyz2[i];
return;
}
int Align::add_align_v(int nadd1, int* add1, int wtm, double* aprv)
{
if (inited==0)
{
printf(" WARNING: in add_align, not init'd \n");
return 0;
}
//revert to initial geometries
for (int i=0;i<3*natoms1;i++)
xyz1[i] = xyz1s[i];
for (int i=0;i<3*natoms2;i++)
xyz2[i] = xyz2s[i];
#if 1
printf(" in add_align_v, adding:");
for (int i=0;i<nadd1;i++)
printf(" %i-%i",add1[2*i+0]+1,add1[2*i+1]+1);
printf("\n");
//printf(" in add_align natoms1: %i natoms2: %i \n",natoms1,natoms2);
#endif
///get v1's for all add atoms
double* v1a = new double[3*nadd1];
for (int i=0;i<3*nadd1;i++) v1a[i] = 0.;
double* v1b = new double[3*nadd1];
for (int i=0;i<3*nadd1;i++) v1b[i] = 0.;
double* c1 = new double[6]; //center points
int* bonded1 = new int[8];
int* bonded2 = new int[8];
int* bonded3 = new int[8];
ICoord ic1,ic2;
ic1.init(natoms1,anames1,anumbers1,xyz1);
ic1.make_frags();
ic1.bond_frags();
//ic1.ic_create_nobonds();
//ic1.print_bonds();
ic2.init(natoms2,anames2,anumbers2,xyz2);
ic2.make_frags();
ic2.bond_frags();
//ic2.ic_create_nobonds();
//ic2.print_bonds();
int npf1 = 0;
int npf2 = 0;
int nvf1 = 0;
int nvf2 = 0;
int found = 0;
for (int i=0;i<nadd1;i++)
{
int a1 = add1[2*i+0];
int a2 = add1[2*i+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
int same_frag = check_frag(a1,a2);
//printf(" a1: %i a2: %i same_frag: %i \n",a1+1,a2+1,same_frag);
a2 -= natoms1;
if (!same_frag)
{
found = 1;
int nbondsa1, nbondsa2;
nbondsa1 = get_bonds(a1,ic1,bonded1);
nbondsa2 = get_bonds(a2,ic2,bonded2);
//first atom's vector
for (int j=0;j<nbondsa1;j++)
{
v1a[3*nvf1+0] += xyz1[3*a1+0] - xyz1[3*bonded1[j]+0];
v1a[3*nvf1+1] += xyz1[3*a1+1] - xyz1[3*bonded1[j]+1];
v1a[3*nvf1+2] += xyz1[3*a1+2] - xyz1[3*bonded1[j]+2];
}
#if 0
if (nbondsa1==1 && ic1.coordn[bonded1[0]]==3)
{
int a1c = bonded1[0];
int nbondsa1c = get_bonds(a1c,ic1,bonded3)
double imptorv = ic1.torsion_val(bonded3[0],a1,bonded3[1],bonded3[2]);
//printf(" imptorv: %4.2f \n",imptorv);
if (fabs(imptorv)>175.)
{
//printf(" using oop v1 \n");
planar_cross(&v1a[3*nvf1],a3,bonded3,xyz1);
}
}
#endif
if (nbondsa1==2)
{
double anglev = ic1.angle_val(bonded1[0],a1,bonded1[1]);
if (anglev>175.)
{
//printf(" using ool v1 \n");
linear_right(&v1a[3*nvf1],a1,bonded1,xyz1);
}
}
if (nbondsa1==3)
{
double imptorv = ic1.torsion_val(bonded1[0],a1,bonded1[1],bonded1[2]);
//printf(" imptorv: %4.2f \n",imptorv);
if (fabs(imptorv)>175.)
{
//printf(" using oop v1 \n");
planar_cross(&v1a[3*nvf1],a1,bonded1,xyz1);
npf1++;
}
}
if (npf1>1)
{
align_v1(nvf1+1,v1a);
}
double n1 = norm(&v1a[3*nvf1],3);
for (int j=0;j<3;j++)
v1a[3*nvf1+j] = v1a[3*nvf1+j] / n1;
#if 0
printf(" v1a(a1): \n");
for (int j=0;j<3;j++)
printf(" %4.3f",v1a[3*nvf1+j]);
printf("\n");
#endif
nvf1++;
//second atom's vector
for (int j=0;j<nbondsa2;j++)
{
v1b[3*nvf2+0] += xyz2[3*a2+0] - xyz2[3*bonded2[j]+0];
v1b[3*nvf2+1] += xyz2[3*a2+1] - xyz2[3*bonded2[j]+1];
v1b[3*nvf2+2] += xyz2[3*a2+2] - xyz2[3*bonded2[j]+2];
}
if (nbondsa2==2)
{
double anglev = ic2.angle_val(bonded2[0],a2,bonded2[1]);
if (anglev>175.)
{
//printf(" using ool v1 (linear angle found) \n");
linear_right(&v1b[3*nvf2],a2,bonded2,xyz2);
}
}
if (nbondsa2==3)
{
double imptorv = ic2.torsion_val(bonded2[0],a2,bonded2[1],bonded2[2]);
//printf(" imptorv: %4.2f \n",imptorv);
if (fabs(imptorv)>175.)
{
//printf(" using oop v1 (planar atom found) \n");
planar_cross(&v1b[3*nvf2],a2,bonded2,xyz2);
npf2++;
}
}
if (npf2>1)
{
align_v1(nvf2+1,v1b);
}
n1 = norm(&v1b[3*nvf2],3);
for (int j=0;j<3;j++)
v1b[3*nvf2+j] = v1b[3*nvf2+j] / n1;
#if 0
printf(" v1b(a2): \n");
for (int j=0;j<3;j++)
printf(" %4.3f",v1b[3*nvf2+j]);
printf("\n");
#endif
nvf2++;
} // if !same_frag
} //loop i over nadd
if (!found)
{
//printf(" couldn't find anything to align \n");
return 0;
}
#if 0
//CPMZ NOT IMPLEMENTED
if (npf1>0)
point_out(v1a,natoms1,xyz1);
if (npf2>0)
point_out(v1b,natoms2,xyz2);
#endif
//averaging over v1 to get v2
double* v2 = new double[6];
for (int i=0;i<6;i++) v2[i] = 0.;
for (int i=0;i<nadd1;i++)
{
for (int j=0;j<3;j++)
v2[j] += v1a[3*i+j];
for (int j=0;j<3;j++)
v2[3+j] += v1b[3*i+j];
}
double n1 = norm(v2,3);
double n2 = norm(&v2[3],3);
if (n1<0.000001)
{
int a1 = add1[2*(nadd1-1)+0];
int a2 = add1[2*(nadd1-1)+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
int nbondsa1 = get_bonds(a1,ic1,bonded1);
linear_right(v2,a1,bonded1,xyz1);
n1 = norm(v2,3);
// printf(" new norm: %8.6f \n",n1);
}
if (n2<0.000001)
{
int a1 = add1[2*(nadd1-1)+0];
int a2 = add1[2*(nadd1-1)+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
a2 -= natoms1;
int nbondsa2 = get_bonds(a2,ic2,bonded2);
linear_right(&v2[3],a2,bonded2,xyz2);
n2 = norm(&v2[3],3);
// printf(" new norm: %8.6f \n",n2);
}
for (int i=0;i<3;i++)
v2[i] = v2[i] / n1;
for (int i=3;i<6;i++)
v2[i] = v2[i] / n2;
#if 0
printf(" v2(1):");
for (int j=0;j<3;j++)
printf(" %4.3f",v2[j]);
printf("\n");
printf(" v2(2):");
for (int j=0;j<3;j++)
printf(" %4.3f",v2[3+j]);
printf("\n");
#endif
//get central location for each
int cfound = 0;
for (int i=0;i<6;i++) c1[i] = 0.;
for (int i=0;i<nadd1;i++)
{
int a1 = add1[2*i+0];
int a2 = add1[2*i+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
int same_frag = check_frag(a1,a2);
a2 -= natoms1;
if (!same_frag)
{
//printf(" c1 for %i-%i \n",a1+1,a2+1);
cfound++;
for (int j=0;j<3;j++)
c1[j] += xyz1[3*a1+j];
for (int j=0;j<3;j++)
c1[3+j] += xyz2[3*a2+j];
}
} //loop i over nadd
if (cfound>1)
for (int j=0;j<6;j++)
c1[j] = c1[j] / cfound;
#if 0
printf(" c1:");
for (int j=0;j<6;j++)
printf(" %4.3f",c1[j]);
printf("\n");
#endif
//find TM fragment, replace c1 and v terms with wtm center and aprv
int f1 = 0;
for (int i=0;i<natoms1;i++)
if (ic1.isTM(i))
f1 = 1;
int f2 = 0;
for (int i=0;i<natoms2;i++)
if (ic2.isTM(i))
f2 = 1;
int TMaddo = 0; //is TM adding to other reactant?
for (int i=0;i<nadd1;i++)
{
int a1 = add1[2*i+0];
int a2 = add1[2*i+1];
int tmp = a1; if (a1>a2) { a1 = a2; a2 = tmp; }
int same_frag = check_frag(a1,a2);
//printf(" a1: %i a2: %i same_frag: %i \n",a1+1,a2+1,same_frag);
a2 -= natoms1;
if (!same_frag)
{
if (ic1.isTM(a1))
{
TMaddo++;
f1++;
}
if (ic2.isTM(a2))
{
TMaddo++;
f2++;
}
}
}
//printf(" fragment with TM: %i %i add across TM-other: %i \n",f1,f2,TMaddo);
if (f1==f2 && TMaddo)
{
printf(" ERROR: neither or both fragments have TMs! \n");
exit(1);
}
else if (f1>0 && TMaddo)
{
c1[0] = xyz1[3*wtm+0];
c1[1] = xyz1[3*wtm+1];
c1[2] = xyz1[3*wtm+2];
v2[0] = aprv[0];
v2[1] = aprv[1];
v2[2] = aprv[2];
}
else if (f2>0 && TMaddo)
{
wtm -= natoms1;
c1[3] = xyz2[3*wtm+0];
c1[4] = xyz2[3*wtm+1];
c1[5] = xyz2[3*wtm+2];
v2[3] = aprv[0];
v2[4] = aprv[1];
v2[5] = aprv[2];
}
else
printf(" not using TM-specific vector \n");
#if 0
printf(" TM c1:");
for (int j=0;j<6;j++)
printf(" %4.3f",c1[j]);
printf("\n");
#endif
#if 0
printf(" TM v2(1):");
for (int j=0;j<3;j++)
printf(" %4.3f",v2[j]);
printf("\n");
printf(" TM v2(2):");
for (int j=0;j<3;j++)
printf(" %4.3f",v2[3+j]);
printf("\n");
#endif
//move geometry to center
double* xyz1a = new double[3*(natoms1+2)];
double* xyz2a = new double[3*(natoms2+2)];
string* anames1a = new string[natoms1+2];
string* anames2a = new string[natoms2+2];
for (int i=0;i<natoms1;i++) anames1a[i] = anames1[i];
anames1a[natoms1] = "X";
anames1a[natoms1+1] = "X";
for (int i=0;i<natoms2;i++) anames2a[i] = anames2[i];
anames2a[natoms2] = "X";
anames2a[natoms2+1] = "X";
for (int i=0;i<natoms1;i++)
{
for (int j=0;j<3;j++)
xyz1a[3*i+j] = xyz1[3*i+j] - c1[j];
}
xyz1a[3*(natoms1)+0] = 0.; xyz1a[3*(natoms1)+1] = 0.;
xyz1a[3*(natoms1)+2] = 0.; xyz1a[3*(natoms1+1)+0] = v2[0];
xyz1a[3*(natoms1+1)+1] = v2[1]; xyz1a[3*(natoms1+1)+2] = v2[2];
//print_xyz_gen(natoms1+2,anames1a,xyz1a);
for (int i=0;i<natoms2;i++)
{
for (int j=0;j<3;j++)
xyz2a[3*i+j] = xyz2[3*i+j] - c1[3+j];
}
xyz2a[3*(natoms2)+0] = 0.; xyz2a[3*(natoms2)+1] = 0.;
xyz2a[3*(natoms2)+2] = 0.; xyz2a[3*(natoms2+1)+0] = v2[3];
xyz2a[3*(natoms2+1)+1] = v2[4]; xyz2a[3*(natoms2+1)+2] = v2[5];
//print_xyz_gen(natoms2+2,anames2a,xyz2a);
//align v2 along x/-x direction
int t1 = natoms1;
int t2 = natoms1+1;
align_to_x(natoms1+2,t1,t2,xyz1a,anames1a,1,10.);
t1 = natoms2;
t2 = natoms2+1;
align_to_x(natoms2+2,t1,t2,xyz2a,anames2a,-1,10.);
//print_xyz_gen(natoms1+2,anames1a,xyz1a);
//print_xyz_gen(natoms2+2,anames2a,xyz2a);
//face each other at X Angstroms
double X = 18.;
for (int i=0;i<3*natoms1;i++)
xyz1[i] = xyz1a[i];
for (int i=0;i<3*natoms2;i++)
xyz2[i] = xyz2a[i];
for (int i=0;i<natoms2;i++)
xyz2[3*i+0] += X;
//prepare for vdw opt
string* anamesp = new string[natoms1+natoms2];
int* anumbersp = new int[natoms1+natoms2];
for (int i=0;i<natoms1;i++)
anamesp[i] = anames1[i];
for (int i=0;i<natoms2;i++)
anamesp[natoms1+i] = anames2[i];
for (int i=0;i<natoms1;i++)
anumbersp[i] = anumbers1[i];
for (int i=0;i<natoms2;i++)
anumbersp[natoms1+i] = anumbers2[i];
//full pair geometry, before vdw opt
for (int i=0;i<3*natoms1;i++)
xyza[i] = xyz1[i];
for (int i=0;i<3*natoms2;i++)
xyza[3*natoms1+i] = xyz2[i];
ICoord icp;
icp.init(natoms1+natoms2,anamesp,anumbersp,xyza);
//print_xyz();
//rotate about central axis
if (nadd1>1)
{
int a1 = add1[0];
int a2 = add1[1];
int tmp1 = a1; if (a1>a2) { a1 = a2; a2 = tmp1; }
int a3 = add1[2];
int a4 = add1[3];
int tmp2 = a3; if (a3>a4) { a3 = a4; a4 = tmp2; }
int same_frag = check_frag(a1,a2) + check_frag(a3,a4);
if (!same_frag && a1!=a3 && a2!=a4)
{
double torv = icp.torsion_val(a1,a3,a4,a2);
//printf(" central torv: %4.2f (%i %i %i %i) \n",torv,a1+1,a3+1,a4+1,a2+1);
rotate_around_x(natoms1,natoms2,-torv,icp.coords);
}
}
double* vx = new double[3];
vx[1] = vx[2] = 0.;
vx[0] = 1.0;
vdw_vector_opt(natoms1,natoms2,vx,icp);