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tm.cpp
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// Please see license.txt for licensing and copyright information //
// Author: Paul Zimmerman, University of Michigan //
#include "zstruct.h"
#include "constants.h"
#define OVERRIDE_TYPE 0
#define ANGLE_LINEAR 150.0
//1. test 3 code (2 code probably okay)
//2. test 4 code
//3. write 5 code --> type 0 (need to test alignment)
//4. in add_align_v TM vs not update (done)
//5. double check eta2 breaking tests... ID correct opposites etc
//Note: could call "run" for multiple TM's
void ZStruct::find_linear_pair(int& a1o, int& a2o, int& a1f, int& a2f, int a1, int a2, int a3, int a4, int wtm, ICoord ic1)
{
double* ang = new double[6];
ang[0] = ic1.angle_val(a1,wtm,a2);
ang[1] = ic1.angle_val(a1,wtm,a3);
ang[2] = ic1.angle_val(a1,wtm,a4);
ang[3] = ic1.angle_val(a2,wtm,a3);
ang[4] = ic1.angle_val(a2,wtm,a4);
ang[5] = ic1.angle_val(a3,wtm,a4);
int nmax = -1;
double max = -1.;
for (int i=0;i<6;i++)
if (ang[i]>max)
{
max = ang[i];
nmax = i;
}
if (nmax==0)
{
a1o = a1;
a2o = a2;
a1f = a3;
a2f = a4;
}
else if (nmax==1)
{
a1o = a1;
a2o = a3;
a1f = a2;
a2f = a4;
}
else if (nmax==2)
{
a1o = a1;
a2o = a4;
a1f = a2;
a2f = a3;
}
else if (nmax==3)
{
a1o = a2;
a2o = a3;
a1f = a1;
a2f = a4;
}
else if (nmax==4)
{
a1o = a2;
a2o = a4;
a1f = a1;
a2f = a3;
}
else if (nmax==5)
{
a1o = a3;
a2o = a4;
a1f = a1;
a2f = a2;
}
delete [] ang;
return;
}
int ZStruct::run_4c_om(int wtm, int stm, int nadd, int* adds, int nbrks, int* brks, ICoord ic1, int* nangles, int** angles, double* anglev, int* ntor, int** tor, double* torv, int* napp, double* aprv)
{
int nfound = 0;
printf(" in run_4c_om for naddtm: %i nbrktm: %i \n",nadd,nbrks);
ntor[0] = 0;
nangles[0] = 0;
napp[0] = 1;
//not handling these cases
if (nadd!=2) return 0;
if (nbrks!=0) return 0;
//center align vector at metal
aprv[0] = ic1.coords[3*wtm+0];
aprv[1] = ic1.coords[3*wtm+1];
aprv[2] = ic1.coords[3*wtm+2];
int** btm = ic1.bondstm;
int a1 = btm[0][1];
int a2 = btm[1][1];
int a3 = btm[2][1];
int a4 = btm[3][1];
int a5 = adds[0];
if (adds[0]==wtm)
a5 = adds[1];
int a6 = adds[2];
if (adds[2]==wtm)
a6 = adds[3];
if (nadd==2) //0 or 1 break
{
//find linear pair
int a1o,a2o; //linear pair
int a1f,a2f; //other two atoms
find_linear_pair(a1o,a2o,a1f,a2f,a1,a2,a3,a4,wtm,ic1);
ntor[0] = 0;
nangles[0] = 2;
angles[0][0] = a1f;
angles[0][1] = wtm;
angles[0][2] = a6;
angles[1][0] = a2f;
angles[1][1] = wtm;
angles[1][2] = a5;
anglev[0] = anglev[1] = 180.;
ntor[1] = 0;
nangles[1] = 2;
angles[2][0] = a1f;
angles[2][1] = wtm;
angles[2][2] = a6;
angles[3][0] = a2f;
angles[3][1] = wtm;
angles[3][2] = a5;
anglev[2] = anglev[3] = 180.;
printf(" nadd: 2. angles: %i %i %i and %i %i %i \n",a1f+1,wtm+1,a5+1,a2f+1,wtm+1,a6+1);
nfound = 2;
napp[0] = napp[1] = 1;
get_vec(wtm,a2f,ic1.coords,&aprv[3]);
get_vec(wtm,a1f,ic1.coords,&aprv[6]);
}
else
nfound = 0;
return nfound;
}
int ZStruct::tm_angle_drive(int nr, int nadd, int* adds, int nbrks, int* brks, ICoord ic1, int* nangles, int** angles, double* anglev, int* ntor, int** tor, double* torv, int* active1)
{
printf("\n in tm_angle_drive for nadd: %i nbrks: %i \n",nadd,nbrks);
int nfound = 0;
for (int i=0;i<nadd;i++)
printf(" adding: %2i %2i \n",adds[2*i+0]+1,adds[2*i+1]+1);
for (int i=0;i<nbrks;i++)
printf(" brking: %2i %2i \n",brks[2*i+0]+1,brks[2*i+1]+1);
// ic1.print_xyz();
// ic1.print_bonds();
//find up to two metal centers
int tm1 = -1; int tm2 = -1;
for (int i=0;i<ic1.natoms;i++)
if (ic1.isTM(i))
{
tm1 = i;
break;
}
for (int i=tm1;i<ic1.natoms;i++)
if (ic1.isTM(i) && tm1!=i)
{
tm2 = i;
break;
}
//temporary bimetallic hack, avoids double TM moves
int tmtmadd = 0;
//TM-TM bond add
for (int i=0;i<nadd;i++)
if (ic1.isTM(adds[2*i+0]) && ic1.isTM(adds[2*i+1]))
tmtmadd++;
//2 different TM adds
for (int i=0;i<nadd;i++)
for (int j=0;j<i;j++)
if (ic1.isTM(adds[2*i+0])+ic1.isTM(adds[2*i+1]) &&
ic1.isTM(adds[2*j+0])+ic1.isTM(adds[2*j+1]))
{
int tm1 = adds[2*i+0];
if (!ic1.isTM(tm1))
tm1 = adds[2*i+1];
int tm2 = adds[2*j+0];
if (!ic1.isTM(tm2))
tm2 = adds[2*j+1];
if (tm1!=tm2)
tmtmadd++;
}
if (tmtmadd)
{
printf(" TM-TM bond or 2x TM add, skipping this one \n");
return 0;
}
/* printf(" active:");
for (int i=0;i<ic1.natoms;i++)
printf(" %2i",active1[i]);
printf("\n"); */
int naddtm = 0;
int nbrktm = 0;
int* addtm = new int[2*nadd+1];
int* brktm = new int[2*nbrks+1];
int wtm = get_wtm_addbrktm(nadd,adds,nbrks,brks,ic1,naddtm,addtm,nbrktm,brktm);
//printf(" TM(%s) is atom %i \n",ic1.anames[wtm].c_str(),wtm+1);
int stm;
int coordntm = -1;
int geomtype = -1;
if (wtm==tm1)
{
stm = 1;
coordntm = ic1.nbondstm;
geomtype = determine_geomtype(wtm,stm,coordntm,ic1);
}
else
{
stm = 2;
coordntm = ic1.nbondstm2;
geomtype = determine_geomtype(wtm,stm,coordntm,ic1);
}
printf(" geomtype is: %2i for TM %i with coordntm: %i \n",geomtype,wtm+1,coordntm);
int* napp = new int[10];
double* aprv = new double[50];
int nroute = run_tm(coordntm,geomtype,wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv,active1);
#if 1
printf(" found (%i) angle drivers:",nroute);
for (int nf=0;nf<nroute;nf++)
printf(" %i",nangles[nf]);
printf("\n");
int angc = 0; //count total angles
for (int nf=0;nf<nroute;nf++)
{
for (int i=0;i<nangles[nf];i++)
{
printf(" %i: %2i %2i %2i %4.1f \n",nf+1,angles[angc][0]+1,angles[angc][1]+1,angles[angc][2]+1,anglev[angc]);
angc++;
}
}
#endif
#if 0
printf(" found torsion drivers:");
for (int nf=0;nf<nroute;nf++)
printf(" %i",ntor[nf]);
printf("\n");
int torc = 0; //count total torsions
for (int nf=0;nf<nroute;nf++)
for (int i=0;i<ntor[nf];i++)
printf(" %i: %2i %2i %2i %2i %4.1f \n",nf+1,tor[torc+i][0]+1,tor[torc+i][1]+1,tor[torc+i][2]+1,tor[torc+i][3],torv[torc++ +i]);
#endif
//align and create input files
angc = 0; //torc = 0;
int nappd = 0;
for (int i=0;i<nroute;i++)
{
if (nr>1)
for (int j=0;j<napp[i];j++)
{
printf(" writing input #%i (niso: %4i) \n",j+1,niso);
int index = 3*(nappd+1); nappd++;
int tm_align_used = align1.add_align_v(nadd,adds,wtm,&aprv[index]);
write_initial_xyz(niso,ic1.natoms,ic1.anames,align1.xyza,ic1.q1);
write_ISOMER(niso++,nadd,adds,nbrks,brks,nangles[i],&angles[angc],&anglev[angc],0,NULL,NULL);
//exit(1);
nfound++;
if (!tm_align_used) break;
}
else
{
printf(" writing input #%i (niso: %4i) \n",i+1,niso);
write_initial_xyz(niso,ic1.natoms,ic1.anames,ic1.coords,ic1.q1);
write_ISOMER(niso++,nadd,adds,nbrks,brks,nangles[i],&angles[angc],&anglev[angc],0,NULL,NULL);
nfound++;
}
angc += nangles[i];
//torc += ntor[i];
}
delete [] addtm;
delete [] brktm;
delete [] napp;
delete [] aprv;
return nfound;
}
int ZStruct::run_tm(int coordntm, int geomtype, int wtm, int stm, int naddtm, int* addtm, int nbrktm, int* brktm, ICoord ic1, int* nangles, int** angles, double* anglev, int* ntor, int** tor, double* torv, int* napp, double* aprv, int* active1)
{
int nroute = 0;
#if OVERRIDE_TYPE
nroute = run_4c_om(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv);
#else
if (coordntm==2)
{
if (geomtype==1)
nroute = run_2c_1(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv);
else
nroute = run_2c_0(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv);
}
else if (coordntm==3)
{
if (geomtype==1)
nroute = run_3c_1(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv);
else
nroute = run_3c_0(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv);
}
else if (coordntm==4)
{
if (geomtype==1)
nroute = run_4c_1(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv,active1);
else
nroute = run_4c_0(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv,active1);
}
else if (coordntm==5)
{
if (geomtype==1)
nroute = run_5c_1(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv,active1);
else
{
nroute = run_5c_0(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv,active1);
}
}
else if (coordntm==6)
{
if (geomtype==1)
nroute = run_6c_1(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv,active1);
else
{
printf(" coordntm 6 geomtype 0 not implemented, using type 1 instead \n");
nroute = run_6c_1(wtm,stm,naddtm,addtm,nbrktm,brktm,ic1,nangles,angles,anglev,ntor,tor,torv,napp,aprv,active1);
// exit(1);
}
}
else
printf(" haven't yet implemented coordntm: %i \n",coordntm);
#endif
return nroute;
}
int ZStruct::run_6c_1(int wtm, int stm, int nadd, int* adds, int nbrks, int* brks, ICoord ic1, int* nangles, int** angles, double* anglev, int* ntor, int** tor, double* torv, int* napp, double* aprv, int* active1)
{
int nfound = 0;
printf(" in run_6c_1 for naddtm: %i nbrktm: %i \n",nadd,nbrks);
ntor[0] = 0;
nangles[0] = 0;
napp[0] = 1;
//not handling these cases
if (nbrks>2 || nadd>2) return 0;
if (nadd>0 && nbrks==0) return 0;
//center align vector at metal
aprv[0] = ic1.coords[3*wtm+0];
aprv[1] = ic1.coords[3*wtm+1];
aprv[2] = ic1.coords[3*wtm+2];
int** btm = ic1.bondstm;
if (stm==2)
btm = ic1.bondstm2;
int a1 = btm[0][1];
int a2 = btm[1][1];
int a3 = btm[2][1];
int a4 = btm[3][1];
int a5 = btm[4][1];
int a6 = btm[5][1];
//int p11,p12,p13,p14; //avoided using this
//int p21,p22,p23,p24;
//int p31,p32,p33,p34;
//find_oct_planes(wtm,ic1,p11,p12,p13,p14,p21,p22,p23,p24,p31,p32,p33,p34);
if (eta2_double_break(wtm,stm,6,nbrks,brks,ic1))
nbrks--;
if (nadd==1 && nbrks==1)
{
int a7 = adds[0];
if (adds[0]==wtm)
a7 = adds[1];
int b1 = brks[0];
if (brks[0]==wtm)
b1 = brks[1];
int b1o = find_opp(b1,wtm,stm,ic1);
int b1s1,b1s2;
find_2_at_90(b1s1,b1s2,b1,b1o,wtm,stm,ic1);
printf(" opposite atom: %2i(%s) 90's: %i %i \n",b1o+1,ic1.anames[b1o].c_str(),b1s1+1,b1s2+1);
ntor[0] = 0;
nangles[0] = 1;
angles[0][0] = a7;
angles[0][1] = wtm;
angles[0][2] = b1o;
anglev[0] = 180.;
nfound = 1;
napp[0] = napp[1] = 4;
get_vec_45p(b1,wtm,b1s1,ic1.coords,&aprv[3]);
get_vec_45m(b1,wtm,b1s1,ic1.coords,&aprv[6]);
get_vec_45p(b1,wtm,b1s2,ic1.coords,&aprv[9]);
get_vec_45m(b1,wtm,b1s2,ic1.coords,&aprv[12]);
} //add1/brk1
else if (nadd==1 && nbrks==2)
{
int a7 = adds[0];
if (adds[0]==wtm)
a7 = adds[1];
int b1 = brks[0];
if (brks[0]==wtm)
b1 = brks[1];
int b2 = brks[2];
if (brks[2]==wtm)
b2 = brks[3];
int b1o = find_opp(b1,wtm,stm,ic1);
int b2o = find_opp(b2,wtm,stm,ic1);
int b1s1,b1s2,b2s1,b2s2;
find_2_at_90(b1s1,b1s2,b1,b1o,wtm,stm,ic1);
find_2_at_90(b2s1,b2s2,b2,b2o,wtm,stm,ic1);
printf(" opposite atom: %2i(%s) 90's: %i %i \n",b1o+1,ic1.anames[b1o].c_str(),b1s1+1,b1s2+1);
printf(" opposite atom: %2i(%s) 90's: %i %i \n",b2o+1,ic1.anames[b2o].c_str(),b2s1+1,b2s2+1);
ntor[0] = ntor[1] = 0;
nangles[0] = nangles[1] = 1;
angles[0][0] = a7;
angles[0][1] = wtm;
angles[0][2] = b1o;
anglev[0] = 180.;
angles[1][0] = a7;
angles[1][1] = wtm;
angles[1][2] = b2o;
anglev[1] = 180.;
nfound = 2;
napp[0] = napp[1] = 4;
get_vec_45p(b1,wtm,b1s1,ic1.coords,&aprv[3]);
get_vec_45m(b1,wtm,b1s1,ic1.coords,&aprv[6]);
get_vec_45p(b1,wtm,b1s2,ic1.coords,&aprv[9]);
get_vec_45m(b1,wtm,b1s2,ic1.coords,&aprv[12]);
get_vec_45p(b2,wtm,b2s1,ic1.coords,&aprv[15]);
get_vec_45m(b2,wtm,b2s1,ic1.coords,&aprv[18]);
get_vec_45p(b2,wtm,b2s2,ic1.coords,&aprv[21]);
get_vec_45m(b2,wtm,b2s2,ic1.coords,&aprv[24]);
} //add1/brk2
else
nfound = 1;
return nfound;
}
void ZStruct::find_2_at_90(int& a1s1, int& a1s2, int a1, int a1o, int wtm, int stm, ICoord ic1)
{
int* attached = new int[12];
int nattached = find_attached(wtm,stm,ic1,attached);
int found = 0;
for (int i=0;i<nattached;i++)
if (attached[i]!=a1 && attached[i]!=a1o && !found)
{
double ang1 = ic1.angle_val(a1,wtm,attached[i]);
if (ang1<ANGLE_LINEAR)
for (int j=0;j<i;j++)
if (attached[j]!=a1 && attached[j]!=a1o)
{
double ang2a = ic1.angle_val(a1,wtm,attached[j]);
double ang2b = ic1.angle_val(attached[i],wtm,attached[j]);
if (ang2a<ANGLE_LINEAR && ang2b<ANGLE_LINEAR)
{
a1s1 = attached[i];
a1s2 = attached[j];
break;
}
}
}
delete [] attached;
return;
}
int ZStruct::find_opp(int a1, int wtm, int stm, ICoord ic1)
{
int a1o = 0;
int* attached = new int[12];
int nattached = find_attached(wtm,stm,ic1,attached);
double maxang = 0.;
for (int i=0;i<nattached;i++)
if (attached[i]!=a1)
{
double ang1 = ic1.angle_val(a1,wtm,attached[i]);
if (ang1>maxang)
{
a1o = attached[i];
maxang = ang1;
}
}
delete [] attached;
return a1o;
}
void ZStruct::find_tb_5c(int* a, int wtm, int stm, ICoord ic1)
{
//printf(" in find_tb_5c for wtm %i stm %i \n",wtm,stm);
int* attached = new int[10];
int** btm = ic1.bondstm;
if (stm==2)
btm = ic1.bondstm2;
int nattached = 5;
for (int i=0;i<5;i++)
attached[i] = btm[i][1];
int a1 = -1;
int a2 = -1;
double maxang = 0.;
for (int i=0;i<nattached;i++)
for (int j=0;j<i;j++)
{
double val1 = ic1.angle_val(attached[i],wtm,attached[j]);
if (val1>maxang)
{
a1 = attached[i];
a2 = attached[j];
maxang = val1;
}
}
a[0] = a1;
a[1] = a2;
int nf = 2;
for (int i=0;i<nattached;i++)
if (a[0]!=attached[i] && a[1]!=attached[i])
a[nf++] = attached[i];
printf(" maximum angle is: %6.3f for %i-%i \n",maxang,a[0]+1,a[1]+1);
if (nf!=5)
{
printf(" ERROR: couldn't determine trigonal planar attachment structure \n");
exit(1);
}
delete [] attached;
return;
}
int ZStruct::run_5c_0(int wtm, int stm, int nadd, int* adds, int nbrks, int* brks, ICoord ic1, int* nangles, int** angles, double* anglev, int* ntor, int** tor, double* torv, int* napp, double* aprv, int* active1)
{
int nfound = 0;
printf(" in run_5c_0 for naddtm: %i nbrktm: %i \n",nadd,nbrks);
ntor[0] = 0;
nangles[0] = 0;
napp[0] = 1;
//not handling these cases
if (nbrks>2 || nadd>2) return 0;
if (nadd==2 && nbrks==0) return 0;
//center align vector at metal
aprv[0] = ic1.coords[3*wtm+0];
aprv[1] = ic1.coords[3*wtm+1];
aprv[2] = ic1.coords[3*wtm+2];
int** btm = ic1.bondstm;
if (stm==2)
btm = ic1.bondstm2;
int a1 = btm[0][1];
int a2 = btm[1][1];
int a3 = btm[2][1];
int a4 = btm[3][1];
int a5 = btm[4][1];
int* a1tb = new int[5];
find_tb_5c(a1tb,wtm,stm,ic1);
int a1t = a1tb[0]; //above
int a1b = a1tb[1]; //below
int a1s1 = a1tb[2];
int a1s2 = a1tb[3];
int a1s3 = a1tb[4];
delete [] a1tb;
printf(" a1t a1b: %i %i a1s's: %i %i %i \n",a1t+1,a1b+1,a1s1+1,a1s2+1,a1s3+1);
//printf(" a's: %i %i %i %i %i ao's: %i %i %i %i \n",a1t+1,a2s+1,a3s+1,a4s+1,a5s+1,a2o+1,a3o+1,a4o+1,a5o+1);
if (eta2_double_break(wtm,stm,5,nbrks,brks,ic1))
nbrks--;
if (nadd==1 && nbrks!=1)
{
int a6 = adds[0];
if (adds[0]==wtm)
a6 = adds[1];
ntor[0] = ntor[1] = ntor[2] = 0;
nangles[0] = nangles[1] = nangles[2] = 1;
//3 destinations/approaches from between trigonal ligands
angles[0][0] = a1s1;
angles[0][1] = wtm;
angles[0][2] = a6;
anglev[0] = 180.;
angles[1][0] = a1s2;
angles[1][1] = wtm;
angles[1][2] = a6;
anglev[1] = 180.;
angles[2][0] = a1s3;
angles[2][1] = wtm;
angles[2][2] = a6;
anglev[2] = 180.;
nfound = 3;
napp[0] = napp[1] = napp[2] = 1;
get_vec(wtm,a1s1,ic1.coords,&aprv[3]);
get_vec(wtm,a1s2,ic1.coords,&aprv[6]);
get_vec(wtm,a1s3,ic1.coords,&aprv[9]);
}
else if (nadd==1 && nbrks==1)
{
int a6 = adds[0];
if (adds[0]==wtm)
a6 = adds[1];
int a2l = brks[0];
if (brks[0]==wtm)
a2l = brks[1];
//put in trigonal plane where leaving ligand was
if (!(a2l==a1t || a2l==a1b))
{
int a1s1o = a1s1;
int a1s2o = a1s2;
if (a2l==a1s1o)
a1s1o = a1s3;
if (a2l==a1s2o)
a1s2o = a1s3;
ntor[0] = 0;
nangles[0] = 2;
angles[0][0] = a1s1o;
angles[0][1] = wtm;
angles[0][2] = a6;
anglev[0] = 120.;
angles[1][0] = a1s2o;
angles[1][1] = wtm;
angles[1][2] = a6;
anglev[1] = 120.;
nfound = 1;
napp[0] = napp[1] = 2;
get_vec(wtm,a1s1o,ic1.coords,&aprv[3]);
get_vec(wtm,a1s2o,ic1.coords,&aprv[6]);
}
//swap with axial
else
{
int a1o = a1t;
if (a2l==a1o)
a1o = a1b;
ntor[0] = 0;
nangles[0] = 1;
angles[0][0] = a1o;
angles[0][1] = wtm;
angles[0][2] = a6;
anglev[0] = 180.;
nfound = 1;
napp[0] = 3;
get_vec_45p_align(a1s1,wtm,a1s2,a2l,ic1.coords,&aprv[3]);
get_vec_45p_align(a1s2,wtm,a1s1,a2l,ic1.coords,&aprv[6]);
get_vec_45p_align(a1s3,wtm,a1s2,a2l,ic1.coords,&aprv[9]);
}
}
else if (nadd==2 && nbrks==1)
{
int a6 = adds[0];
if (adds[0]==wtm)
a6 = adds[1];
int a7 = adds[2];
if (adds[2]==wtm)
a7 = adds[3];
int a2l = brks[0];
if (brks[0]==wtm)
a2l = brks[1];
//leaving group is in trigonal plane
if (!(a2l==a1t || a2l==a1b))
{
int a1s1o = a1s1;
int a1s2o = a1s2;
if (a2l==a1s1o)
a1s1o = a1s3;
if (a2l==a1s2o)
a1s2o = a1s3;
ntor[0] = ntor[1] = 0;
nangles[0] = nangles[1] = 2;
angles[0][0] = a1s1o;
angles[0][1] = wtm;
angles[0][2] = a6;
anglev[0] = 180.;
angles[1][0] = a1s2o;
angles[1][1] = wtm;
angles[1][2] = a7;
anglev[1] = 180.;
//second attach configuration
angles[2][0] = a1s1o;
angles[2][1] = wtm;
angles[2][2] = a7;
anglev[2] = 180.;
angles[3][0] = a1s2o;
angles[3][1] = wtm;
angles[3][2] = a6;
anglev[3] = 180.;
nfound = 2;
napp[0] = napp[1] = 2;
get_vec(wtm,a1s1o,ic1.coords,&aprv[3]);
get_vec(wtm,a1s2o,ic1.coords,&aprv[6]);
aprv[9] = aprv[3]; aprv[10] = aprv[4]; aprv[11] = aprv[5];
aprv[12] = aprv[6]; aprv[13] = aprv[7]; aprv[14] = aprv[8];
}
//leaving group is axial
else
{
int a1o = a1t; //group opposite leaving group
if (a2l==a1o)
a1o = a1b;
ntor[0] = ntor[1] = 0;
nangles[0] = nangles[1] = 2;
angles[0][0] = a1o;
angles[0][1] = wtm;
angles[0][2] = a6;
anglev[0] = 180.;
angles[1][0] = a1o;
angles[1][1] = wtm;
angles[1][2] = a7;
anglev[1] = 90.;
angles[2][0] = a1o;
angles[2][1] = wtm;
angles[2][2] = a7;
anglev[2] = 180.;
angles[3][0] = a1o;
angles[3][1] = wtm;
angles[3][2] = a6;
anglev[3] = 90.;
nfound = 2;
napp[0] = napp[1] = 3;
get_vec_45p_align(a1s1,wtm,a1s2,a2l,ic1.coords,&aprv[3]);
get_vec_45p_align(a1s2,wtm,a1s1,a2l,ic1.coords,&aprv[6]);
get_vec_45p_align(a1s3,wtm,a1s2,a2l,ic1.coords,&aprv[9]);
aprv[12] = aprv[3]; aprv[13] = aprv[4]; aprv[14] = aprv[5];
aprv[15] = aprv[6]; aprv[16] = aprv[7]; aprv[17] = aprv[8];
aprv[18] = aprv[9]; aprv[19] = aprv[10]; aprv[20] = aprv[11];
}
}
else if (nadd==1 && nbrks==2)
{
int a6 = adds[0];
if (adds[0]==wtm)
a6 = adds[1];
int a2l = brks[0];
if (brks[0]==wtm)
a2l = brks[1];
int a3l = brks[2];
if (brks[2]==wtm)
a3l = brks[3];
printf(" INCOMPLETE: nadd==1 nbrks==2 \n");
printf(" shouldn't be here! \n");
exit(1);
} //1 add, 2 brk
//for nadd==0
else
nfound = 1;
return nfound;
}
int ZStruct::run_5c_1(int wtm, int stm, int nadd, int* adds, int nbrks, int* brks, ICoord ic1, int* nangles, int** angles, double* anglev, int* ntor, int** tor, double* torv, int* napp, double* aprv, int* active1)
{
int nfound = 0;
printf(" in run_5c_1 for naddtm: %i nbrktm: %i \n",nadd,nbrks);
ntor[0] = 0;
nangles[0] = 0;
napp[0] = 1;
//not handling these cases
if (nbrks>2 || nadd>2) return 0;
if (nadd==2 && nbrks==0) return 0;
//center align vector at metal
aprv[0] = ic1.coords[3*wtm+0];
aprv[1] = ic1.coords[3*wtm+1];
aprv[2] = ic1.coords[3*wtm+2];
int** btm = ic1.bondstm;
if (stm==2)
btm = ic1.bondstm2;
int a1 = btm[0][1];
int a2 = btm[1][1];
int a3 = btm[2][1];
int a4 = btm[3][1];
int a5 = btm[4][1];
int a1t = find_on_top_5c(wtm,stm,ic1);
int a2s = a1; //in plane
int a3s = a2;
int a4s = a3;
int a5s = a4;
if (a1==a1t) a2s = a5;
if (a2==a1t) a3s = a5;
if (a3==a1t) a4s = a5;
if (a4==a1t) a5s = a5;
int a2o, a3o, a4o, a5o;
find_linear_pairs(a2o,a3o,a4o,a5o,a2s,a3s,a4s,a5s,wtm,ic1);
//printf(" a's: %i %i %i %i %i ao's: %i %i %i %i \n",a1t+1,a2s+1,a3s+1,a4s+1,a5s+1,a2o+1,a3o+1,a4o+1,a5o+1);
if (eta2_double_break(wtm,stm,5,nbrks,brks,ic1))
nbrks--;
if (nadd>0 && nbrks==0)
{
int a6 = adds[0];
if (adds[0]==wtm)
a6 = adds[1];
ntor[0] = 0;
nangles[0] = 1;
angles[0][0] = a1t;
angles[0][1] = wtm;
angles[0][2] = a6;
anglev[0] = 180.;
if (nadd==2) anglev[0] = 170.;
nfound = 1;
napp[0] = 1;
get_vec(wtm,a1t,ic1.coords,&aprv[3]);
int nf = 0;
int nang = 0;
//4 approaches with shifted equitorial ligands
if (active1[a2s] && nadd==1)
{
int a2c = a3s;
if (a3s==a2o)
a2c = a4s;
ntor[nf+1] = 0;
nangles[nf+1] = 2;
angles[nang+1][0] = a2o;
angles[nang+1][1] = wtm;
angles[nang+1][2] = a6;
angles[nang+2][0] = a2s;
angles[nang+2][1] = wtm;
angles[nang+2][2] = a1t;
anglev[nang+1] = 180.;
anglev[nang+2] = 180.;
napp[nf+1] = 1;
get_vec_45p_align(a2s,wtm,a2c,a1t,ic1.coords,&aprv[(nf+2)*3]);
//align_vec(a1t,wtm,ic1.coords,&aprv[(nf+2)*3]);
nf++;
nang += 2;
nfound++;
}
if (active1[a3s] && nadd==1)
{
int a2c = a2s;
if (a3s==a3o)
a2c = a4s;
ntor[nf+1] = 0;
nangles[nf+1] = 2;
angles[nang+1][0] = a3o;
angles[nang+1][1] = wtm;
angles[nang+1][2] = a6;
angles[nang+2][0] = a3s;
angles[nang+2][1] = wtm;
angles[nang+2][2] = a1t;
anglev[nang+1] = 180.;
anglev[nang+2] = 180.;
napp[nf+1] = 1;
get_vec_45p_align(a3s,wtm,a2c,a1t,ic1.coords,&aprv[(nf+2)*3]);
//align_vec(a1t,wtm,ic1.coords,&aprv[(nf+2)*3]);
nf++;
nang += 2;
nfound++;
}
if (active1[a4s] && nadd==1)
{
int a2c = a2s;
if (a2s==a4o)
a2c = a3s;
ntor[nf+1] = 0;
nangles[nf+1] = 2;
angles[nang+1][0] = a4o;