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base_pair.cpp
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base_pair.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Daniel Hinckley (Wisconsin/UChicago) dhinckley@wisc.edu
------------------------------------------------------------------------- */
#include "math.h"
#include "atom.h"
#include "stdio.h"
#include "stdlib.h"
#include "math_const.h"
#include "base_pair.h"
#include "memory.h"
#include "error.h"
#include "string.h"
#include "domain.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SIX 6
#define THREE 3
#define SMALL 10E-6
#define EMPTY -12345
/* ---------------------------------------------------------------------- */
// My constructor
BasePair::BasePair(LAMMPS *lmp) : Pointers(lmp){}
/* ---------------------------------------------------------------------- */
// My destructor
BasePair::~BasePair()
{
}
/* ---------------------------------------------------------------------- */
void BasePair::assign(int *indices, int *site_type, double ***param, double ***angle,double **x)
{
double athe[6], cnum;
int debug = 0;
int i,j;
int typa,typb,typc,typd,type, typf;
// Schematic of layout for all sites
/* A drawing of the system
a====b ---- d====c --> The Hydrogen Bond
\ /
Q1 \ / Q2
\/ Cross stacking interactions
/\
/ \
/ \
f e
*/
// Storing the indices in a local array
stea = indices[0];
steb = indices[1];
stec = indices[2];
sted = indices[3];
stee = indices[4];
stef = indices[5];
typa = site_type[0];
typb = site_type[1];
typc = site_type[2];
typd = site_type[3];
type = site_type[4];
typf = site_type[5];
// Get relevant angles, sigm, and epsilon
if ((typb != EMPTY) && (typd != EMPTY))
ateq[0] = angle[0][typb][typd]; // Angle between ba and dc
if ((typb != EMPTY) && (type != EMPTY))
ateq[1] = angle[1][typb][type]; // Angle between ba and be
if ((typb != EMPTY) && (typf != EMPTY))
ateq[2] = angle[2][typd][typf]; // Angle between dc and df
if ((typb != EMPTY) && (typd != EMPTY))
ateq[3] = angle[3][typb][typd]; // Torsion angle created by a-b-d-c
if ((typb != EMPTY) && (typd != EMPTY))
ateq[4] = angle[4][typb][typd]; // Angle between a-b-d
if ((typb != EMPTY) && (typd != EMPTY))
ateq[5] = angle[5][typb][typd]; // Angle between b-d-c
for (i = 0; i < 5; i++)
{
////printf("angle %d = %lf ",i+1,ateq[i]);
}
// Checking to make sure there aren't any issues
for (i = 0; i < SIX; i++)
{
// if (ateq[i] == EMPTY) error->all(FLERR,"EMPTY value for equilibrium angle %d",i); // Throw error
}
// Storing the sigmas that we need
j = 0; // First cross-stacking interaction
if ((typb != EMPTY) && (type != EMPTY)){
sigm[j] = param[j][typb][type];
alpha[j] = param[j+3][typb][type];
range[j] = param[j+6][typb][type];
epsi[j] = param[j+9][typb][type];
}
j++; // Second cross-stacking interaction
if ((typd != EMPTY) && (typf != EMPTY)){
sigm[j] = param[j][typd][typf];
alpha[j] = param[j+3][typd][typf];
range[j] = param[j+6][typd][typf];
epsi[j] = param[j+9][typd][typf];
}
j++; // Base pairing interaction
if ((typb != EMPTY) && (typd != EMPTY)){
sigm[j] = param[j][typb][typd];
alpha[j] = param[j+3][typb][typd];
range[j] = param[j+6][typb][typd];
epsi[j] = param[j+9][typb][typd];
}
// Checking to make sure there aren't any issues with the values that I have stored
for (i = 0; i < THREE; i++)
{
//if (sigm[i] == EMPTY) error->all(FLERR,"EMPTY value for equilibrium sigma %d",i);
//if (alpha[i] == EMPTY) error->all(FLERR,"EMPTY value for alpha value %d",i);
//if (range[i] == EMPTY) error->all(FLERR,"EMPTY value for range value %d",i);
//if (epsi[i] == EMPTY) error->all(FLERR,"EMPTY value for epsilon %d",i);
}
// These ar
// Compute distances for all interactions and store
// if steX = -1 then arbitratily set to values 1. Value shouldn't be used...
if ((typa != EMPTY) && (typb != EMPTY)){
dbax = x[steb][0] - x[stea][0];
dbay = x[steb][1] - x[stea][1];
dbaz = x[steb][2] - x[stea][2];
}
else dbax = dbay = dbaz = 1;
domain->minimum_image(dbax,dbay,dbaz);
if ((typd != EMPTY) && (typc != EMPTY)){
ddcx = x[sted][0] - x[stec][0];
ddcy = x[sted][1] - x[stec][1];
ddcz = x[sted][2] - x[stec][2];
}
else ddcx = ddcy = ddcz = 1;
domain->minimum_image(ddcx,ddcy,ddcz);
if ((typd != EMPTY) && (typb != EMPTY)){
ddbx = x[sted][0] - x[steb][0];
ddby = x[sted][1] - x[steb][1];
ddbz = x[sted][2] - x[steb][2];
}
else ddbx = ddby = ddbz = 1;
domain->minimum_image(ddbx,ddby,ddbz);
if ((typb != EMPTY) && (type != EMPTY)){
dbex = x[steb][0] - x[stee][0];
dbey = x[steb][1] - x[stee][1];
dbez = x[steb][2] - x[stee][2];
}
else dbex = dbey = dbez = 1;
domain->minimum_image(dbex,dbey,dbez);
if ((typd != EMPTY) && (typf != EMPTY)){
ddfx = x[sted][0] - x[stef][0];
ddfy = x[sted][1] - x[stef][1];
ddfz = x[sted][2] - x[stef][2];
}
else ddfx = ddfy = ddfz = 1;
domain->minimum_image(ddfx,ddfy,ddfz);
// Constructing the relevant unit vectors
dbai = 1.0 / sqrt(dbax * dbax + dbay * dbay + dbaz * dbaz);
ebax = dbax * dbai;
ebay = dbay * dbai;
ebaz = dbaz * dbai;
ddci = 1.0 / sqrt(ddcx * ddcx + ddcy * ddcy + ddcz * ddcz);
edcx = ddcx * ddci;
edcy = ddcy * ddci;
edcz = ddcz * ddci;
ddbi = 1.0 / sqrt(ddbx * ddbx + ddby * ddby + ddbz * ddbz);
edbx = ddbx * ddbi;
edby = ddby * ddbi;
edbz = ddbz * ddbi;
dbei = 1.0 / sqrt(dbex * dbex + dbey * dbey + dbez * dbez);
ebex = dbex * dbei;
ebey = dbey * dbei;
ebez = dbez * dbei;
ddfi = 1.0 / sqrt(ddfx * ddfx + ddfy * ddfy + ddfz * ddfz);
edfx = ddfx * ddfi;
edfy = ddfy * ddfi;
edfz = ddfz * ddfi;
// Store the length of each of these vectors in the class
dba = 1.0/dbai;
ddc = 1.0/ddci;
ddb = 1.0/ddbi;
dbe = 1.0/dbei;
ddf = 1.0/ddfi;
ddbsi = ddbi * ddbi;
dbesi = dbei * dbei;
ddfsi = ddfi * ddfi;
// Calculating the relevant angles
cphi[0] = ebax * edcx + ebay * edcy + ebaz * edcz;
cphi[1] = ebax * ebex + ebay * ebey + ebaz * ebez;
cphi[2] = edcx * edfx + edcy * edfy + edcz * edfz;
padx = ebay * edbz - ebaz * edby;
pady = ebaz * edbx - ebax * edbz;
padz = ebax * edby - ebay * edbx;
cosb = -(ebax * edbx + ebay * edby + ebaz * edbz);
if (cosb > (1. - SMALL)) cosb = (1. - SMALL);
if (cosb < (-1. + SMALL)) cosb = (-1. + SMALL);
isb2 = 1.0 / (1.0 - cosb * cosb);
isnb = sqrt(isb2);
pbcx = edcz * edby - edcy * edbz;
pbcy = edcx * edbz - edcz * edbx;
pbcz = edcy * edbx - edcx * edby;
cosd = (edcx * edbx + edcy * edby + edcz * edbz);
if (cosd > (1. - SMALL)) cosd = (1. - SMALL);
if (cosd < (-1. + SMALL)) cosd = (-1. + SMALL);
isd2 = 1.0 / (1.0 - cosd * cosd);
isnd = sqrt(isd2);
pacx = (padz * pbcy - pady * pbcz);
pacy = (padx * pbcz - padz * pbcx);
pacz = (pady * pbcx - padx * pbcy);
cnum = (pacx * edbx + pacy * edby + pacz * edbz);
cphi[3] =
-(padx * pbcx + pady * pbcy + padz * pbcz) * isnb * isnd;
cphi[4] = ebax * -edbx + ebay * -edby + ebaz * -edbz;
cphi[5] = edbx * edcx + edby * edcy + edbz * edcz;
// Making sure that we avoid anamolous behavior
for (i = 0; i < SIX; i++)
{
if (cphi[i] > (1. - SMALL)) cphi[i] = (1. - SMALL);
if (cphi[i] < (-1. + SMALL)) cphi[i] = (-1. + SMALL);
athe[i] = acos(cphi[i]);
}
// Residual code... not sure if necessary
if (cnum < 0.0)
{
athe[3] = -athe[3];
}
for (i = 0; i < SIX; i++)
{
dtha[i] = athe[i] - ateq[i];
}
// Finished initializing all values need for interactions
}
/* ---------------------------------------------------------------------- */
double BasePair::cross_stacking(int c, double**f)
{
// Calculate the possible cross stacking interactions
/*
c == 0 cstk1
c == 1 cstk2
*/
int ibp;
double cos2, sin2, ctrm, bptrm, pref, pref2, ecstk;
double frce, engy;
double fr1x, fr1y, fr1z, fr2x, fr2y, fr2z, fr3x, fr3y, fr3z,
fr4x, fr4y, fr4z, fr5x, fr5y, fr5z;
fr1x = fr1y = fr1z = 0.0;
fr2x = fr2y = fr2z = 0.0;
fr3x = fr3y = fr3z = 0.0;
fr4x = fr4y = fr4z = 0.0;
fr5x = fr5y = fr5z = 0.0;
ibp = 2;
ecstk = 0.0;
// Calculate the a - b - e cross-stacking interaction
if (!c)
{
if ( (dtha[0] >= -MY_PI/(range[ibp]*2.0)) && (dtha[0] <= MY_PI/(range[ibp]*2.0)))
{
if ( (dtha[c+1] >= -MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/(range[c]*2.0)))
{
mors_norp(dbesi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += engy;
f[stee][0] -= frce * dbex;
f[stee][1] -= frce * dbey;
f[stee][2] -= frce * dbez;
f[steb][0] += frce * dbex;
f[steb][1] += frce * dbey;
f[steb][2] += frce * dbez;
}
else if (((dtha[c+1] >= MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/range[c])) || ((dtha[c+1] <= -MY_PI/(range[c]*2.0)) && (dtha[c+1] >= -MY_PI/range[c])))
{
cos2 = cos(range[c]*dtha[c+1]);
sin2 = sin(range[c]*dtha[c+1]);
ctrm = 1.0 - cos2 * cos2;
mors_norp(dbesi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += ctrm * engy;
pref2 = 2.0 * range[c] * cos2 * sin2 * 1.0 /sqrt(1.0-cphi[c+1]*cphi[c+1]);
// 1 site A
fr1x = pref2 * (dbai * (cphi[c+1] * ebax - ebex)) * engy;
fr1y = pref2 * (dbai * (cphi[c+1] * ebay - ebey)) * engy;
fr1z = pref2 * (dbai * (cphi[c+1] * ebaz - ebez)) * engy;
// 2 site B
fr2x = pref2 * (dbai * (ebex - ebax * cphi[c+1] ) + dbei * (ebax - cphi[c+1] * ebex)) * engy + ctrm * dbex * frce;
fr2y = pref2 * (dbai * (ebey - ebay * cphi[c+1] ) + dbei * (ebay - cphi[c+1] * ebey)) * engy + ctrm * dbey * frce;
fr2z = pref2 * (dbai * (ebez - ebaz * cphi[c+1] ) + dbei * (ebaz - cphi[c+1] * ebez)) * engy + ctrm * dbez * frce;
// 3 site E
fr3x = pref2 * (dbei * (ebex * cphi[c+1] - ebax)) * engy - ctrm * dbex * frce;
fr3y = pref2 * (dbei * (ebey * cphi[c+1] - ebay)) * engy - ctrm * dbey * frce;
fr3z = pref2 * (dbei * (ebez * cphi[c+1] - ebaz)) * engy - ctrm * dbez * frce;
f[stea][0] += fr1x;
f[stea][1] += fr1y;
f[stea][2] += fr1z;
f[steb][0] += fr2x;
f[steb][1] += fr2y;
f[steb][2] += fr2z;
f[stee][0] += fr3x;
f[stee][1] += fr3y;
f[stee][2] += fr3z;
}
else if ((dtha[c+1] > MY_PI/range[c]) || (dtha[c+1] < -MY_PI/range[c]))
{
}
}
else if (((dtha[0] >= MY_PI/(range[ibp]*2.0)) && (dtha[0] <= MY_PI/range[ibp])) || ((dtha[0] <= -MY_PI/(range[ibp]*2.0)) && (dtha[0] >= -MY_PI/range[ibp])))
{
cos2 = cos(range[ibp]*dtha[0]);
sin2 = sin(range[ibp]*dtha[0]);
bptrm = 1.0 - cos2 * cos2;
pref = 2.0 * range[ibp] * cos2 * sin2 * 1.0 /sqrt(1.0-cphi[0]*cphi[0]);
if ( (dtha[c+1] >= -MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/(range[c]*2.0)))
{
mors_norp(dbesi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += bptrm * engy;
// Site A
fr1x = pref * dbai * (ebax * cphi[0] - edcx) * engy;
fr1y = pref * dbai * (ebay * cphi[0] - edcy) * engy;
fr1z = pref * dbai * (ebaz * cphi[0] - edcz) * engy;
// Site B
fr2x = pref * dbai * (edcx - ebax * cphi[0]) * engy + bptrm * dbex * frce;
fr2y = pref * dbai * (edcy - ebay * cphi[0]) * engy + bptrm * dbey * frce;
fr2z = pref * dbai * (edcz - ebaz * cphi[0]) * engy + bptrm * dbez * frce;
// Site C
fr3x = pref * ddci * (edcx * cphi[0] - ebax) * engy;
fr3y = pref * ddci * (edcy * cphi[0] - ebay) * engy;
fr3z = pref * ddci * (edcz * cphi[0] - ebaz) * engy;
// Site D
fr4x = pref * ddci * (ebax - edcx * cphi[0]) * engy;
fr4y = pref * ddci * (ebay - edcy * cphi[0]) * engy;
fr4z = pref * ddci * (ebaz - edcz * cphi[0]) * engy;
// Site E
fr5x = -bptrm * dbex * frce;
fr5y = -bptrm * dbey * frce;
fr5z = -bptrm * dbez * frce;
f[stea][0] += fr1x;
f[stea][1] += fr1y;
f[stea][2] += fr1z;
f[steb][0] += fr2x;
f[steb][1] += fr2y;
f[steb][2] += fr2z;
f[stec][0] += fr3x;
f[stec][1] += fr3y;
f[stec][2] += fr3z;
f[sted][0] += fr4x;
f[sted][1] += fr4y;
f[sted][2] += fr4z;
f[stee][0] += fr5x;
f[stee][1] += fr5y;
f[stee][2] += fr5z;
}
else if (((dtha[c+1] >= MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/range[c])) || ((dtha[c+1] <= -MY_PI/(range[c]*2.0)) && (dtha[c+1] >= -MY_PI/range[c])))
{
cos2 = cos(range[c]*dtha[c+1]);
sin2 = sin(range[c]*dtha[c+1]);
ctrm = 1.0 - cos2 * cos2;
pref2 = 2.0 * range[c] * cos2 * sin2 * 1.0 /sqrt(1.0-cphi[c+1]*cphi[c+1]);
mors_norp(dbesi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += bptrm * ctrm * engy;
// The potential is modulated by the angle for the hydrogen bonding
// Site A
fr1x = pref * dbai * (ebax * cphi[0] - edcx) * ctrm * engy + pref2 * (dbai * (ebax * cphi[c+1] - ebex)) * bptrm * engy;
fr1y = pref * dbai * (ebay * cphi[0] - edcy) * ctrm * engy + pref2 * (dbai * (ebay * cphi[c+1] - ebey)) * bptrm * engy;
fr1z = pref * dbai * (ebaz * cphi[0] - edcz) * ctrm * engy + pref2 * (dbai * (ebaz * cphi[c+1] - ebez)) * bptrm * engy;
// Site B
fr2x = pref * dbai * (edcx - ebax * cphi[0]) * ctrm * engy + pref2 * (dbai * (ebex - cphi[c+1] * ebax) + dbei * (ebax - cphi[c+1] * ebex)) * bptrm * engy + bptrm * ctrm * dbex * frce;
fr2y = pref * dbai * (edcy - ebay * cphi[0]) * ctrm * engy + pref2 * (dbai * (ebey - cphi[c+1] * ebay) + dbei * (ebay - cphi[c+1] * ebey)) * bptrm * engy + bptrm * ctrm * dbey * frce;
fr2z = pref * dbai * (edcz - ebaz * cphi[0]) * ctrm * engy + pref2 * (dbai * (ebez - cphi[c+1] * ebaz) + dbei * (ebaz - cphi[c+1] * ebez)) * bptrm * engy + bptrm * ctrm * dbez * frce;
// Site C
fr3x = pref * ddci * (edcx * cphi[0] - ebax) * ctrm * engy;
fr3y = pref * ddci * (edcy * cphi[0] - ebay) * ctrm * engy;
fr3z = pref * ddci * (edcz * cphi[0] - ebaz) * ctrm * engy;
// Site D
fr4x = pref * ddci * (ebax - edcx * cphi[0]) * ctrm * engy;
fr4y = pref * ddci * (ebay - edcy * cphi[0]) * ctrm * engy;
fr4z = pref * ddci * (ebaz - edcz * cphi[0]) * ctrm * engy;
// Site E
fr5x = pref2 * (dbei * (ebex * cphi[c+1] - ebax)) * bptrm * engy - bptrm * ctrm * dbex * frce ;
fr5y = pref2 * (dbei * (ebey * cphi[c+1] - ebay)) * bptrm * engy - bptrm * ctrm * dbey * frce ;
fr5z = pref2 * (dbei * (ebez * cphi[c+1] - ebaz)) * bptrm * engy - bptrm * ctrm * dbez * frce ;
f[stea][0] += fr1x;
f[stea][1] += fr1y;
f[stea][2] += fr1z;
f[steb][0] += fr2x;
f[steb][1] += fr2y;
f[steb][2] += fr2z;
f[stec][0] += fr3x;
f[stec][1] += fr3y;
f[stec][2] += fr3z;
f[sted][0] += fr4x;
f[sted][1] += fr4y;
f[sted][2] += fr4z;
f[stee][0] += fr5x;
f[stee][1] += fr5y;
f[stee][2] += fr5z;
}
else if ((dtha[c+1] > MY_PI/range[c]) || (dtha[c+1] < -MY_PI/range[c]))
{
}
}
}
// Calculate the other cross stacking interction
if (c == 1)
{
if ( (dtha[0] >= -MY_PI/(range[ibp]*2.0)) && (dtha[0] <= MY_PI/(range[ibp]*2.0)))
{
// Now examining the other cross stacking interaction
if ( (dtha[c+1] >= -MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/(range[c]*2.0)))
{
mors_norp(ddfsi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += engy;
// Apply the force
f[stef][0] -= frce * ddfx;
f[stef][1] -= frce * ddfy;
f[stef][2] -= frce * ddfz;
f[sted][0] += frce * ddfx;
f[sted][1] += frce * ddfy;
f[sted][2] += frce * ddfz;
}
else if (((dtha[c+1] >= MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/range[c])) || ((dtha[c+1] <= -MY_PI/(range[c]*2.0)) && (dtha[c+1] >= -MY_PI/range[c])))
{
cos2 = cos(range[c]*dtha[c+1]);
sin2 = sin(range[c]*dtha[c+1]);
ctrm = 1.0 - cos2 * cos2;
mors_norp(ddfsi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += ctrm * engy;
pref2 = 2.0 * range[c] * cos2 * sin2 * 1.0 /sqrt(1.0-cphi[c+1]*cphi[c+1]);
// 1 site C
fr1x = pref2 * (ddci * (cphi[c+1] * edcx - edfx)) * engy;
fr1y = pref2 * (ddci * (cphi[c+1] * edcy - edfy)) * engy;
fr1z = pref2 * (ddci * (cphi[c+1] * edcz - edfz)) * engy;
// 2 site D
fr2x = pref2 * (ddci * (edfx - cphi[c+1] * edcx) + ddfi * (edcx - cphi[c+1] * edfx)) * engy + ctrm * ddfx * frce;
fr2y = pref2 * (ddci * (edfy - cphi[c+1] * edcy) + ddfi * (edcy - cphi[c+1] * edfy)) * engy + ctrm * ddfy * frce;
fr2z = pref2 * (ddci * (edfz - cphi[c+1] * edcz) + ddfi * (edcz - cphi[c+1] * edfz)) * engy + ctrm * ddfz * frce;
// 3 site F
fr3x = pref2 * (ddfi * (cphi[c+1] * edfx - edcx)) * engy - ctrm * ddfx * frce;
fr3y = pref2 * (ddfi * (cphi[c+1] * edfy - edcy)) * engy - ctrm * ddfy * frce;
fr3z = pref2 * (ddfi * (cphi[c+1] * edfz - edcz)) * engy - ctrm * ddfz * frce;
f[stec][0] += fr1x;
f[stec][1] += fr1y;
f[stec][2] += fr1z;
f[sted][0] += fr2x;
f[sted][1] += fr2y;
f[sted][2] += fr2z;
f[stef][0] += fr3x;
f[stef][1] += fr3y;
f[stef][2] += fr3z;
}
else if ((dtha[c+1] > MY_PI/range[c]) || (dtha[c+1] < -MY_PI/range[c]))
{
}
}
else if (((dtha[0] >= MY_PI/(range[ibp]*2.0)) && (dtha[0] <= MY_PI/range[ibp])) || ((dtha[0] <= -MY_PI/(range[ibp]*2.0)) && (dtha[0] >= -MY_PI/range[ibp])))
{
cos2 = cos(range[ibp]*dtha[0]);
sin2 = sin(range[ibp]*dtha[0]);
bptrm = 1.0 - cos2 * cos2;
pref = 2.0 * range[ibp] * cos2 * sin2 * 1.0 /sqrt(1.0-cphi[0]*cphi[0]);
if ( (dtha[c+1] >= -MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/(range[c]*2.0)))
{
mors_norp(ddfsi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += bptrm * engy;
// The potential is modulated by the angle for the hydrogen bonding
// Site A
fr1x = pref * dbai * (ebax * cphi[0] - edcx) * engy;
fr1y = pref * dbai * (ebay * cphi[0] - edcy) * engy;
fr1z = pref * dbai * (ebaz * cphi[0] - edcz) * engy;
// Site B
fr2x = pref * dbai * (edcx - ebax * cphi[0]) * engy;
fr2y = pref * dbai * (edcy - ebay * cphi[0]) * engy;
fr2z = pref * dbai * (edcz - ebaz * cphi[0]) * engy;
// Site C
fr3x = pref * ddci * (edcx * cphi[0] - ebax) * engy;
fr3y = pref * ddci * (edcy * cphi[0] - ebay) * engy;
fr3z = pref * ddci * (edcz * cphi[0] - ebaz) * engy;
// Site D
fr4x = pref * ddci * (ebax - edcx * cphi[0]) * engy + bptrm * ddfx * frce;
fr4y = pref * ddci * (ebay - edcy * cphi[0]) * engy + bptrm * ddfy * frce;
fr4z = pref * ddci * (ebaz - edcz * cphi[0]) * engy + bptrm * ddfz * frce;
// Site F
fr5x = -bptrm * ddfx * frce;
fr5y = -bptrm * ddfy * frce;
fr5z = -bptrm * ddfz * frce;
f[stea][0] += fr1x;
f[stea][1] += fr1y;
f[stea][2] += fr1z;
f[steb][0] += fr2x;
f[steb][1] += fr2y;
f[steb][2] += fr2z;
f[stec][0] += fr3x;
f[stec][1] += fr3y;
f[stec][2] += fr3z;
f[sted][0] += fr4x;
f[sted][1] += fr4y;
f[sted][2] += fr4z;
f[stef][0] += fr5x;
f[stef][1] += fr5y;
f[stef][2] += fr5z;
}
else if (((dtha[c+1] >= MY_PI/(range[c]*2.0)) && (dtha[c+1] <= MY_PI/range[c])) || ((dtha[c+1] <= -MY_PI/(range[c]*2.0)) && (dtha[c+1] >= -MY_PI/range[c])))
{
cos2 = cos(range[c]*dtha[c+1]);
sin2 = sin(range[c]*dtha[c+1]);
ctrm = 1.0 - cos2 * cos2;
pref2 = 2.0 * range[c] * cos2 * sin2 * 1.0 /sqrt(1.0-cphi[c+1]*cphi[c+1]);
mors_norp(ddfsi, alpha[c], epsi[c], sigm[c], &frce, &engy);
ecstk += bptrm * ctrm * engy;
// The potential is modulated by the angle for the hydrogen bonding
// Site A
fr1x = pref * dbai * (ebax * cphi[0] - edcx) * ctrm * engy;
fr1y = pref * dbai * (ebay * cphi[0] - edcy) * ctrm * engy;
fr1z = pref * dbai * (ebaz * cphi[0] - edcz) * ctrm * engy;
// Site B
fr2x = pref * dbai * (edcx - ebax * cphi[0]) * ctrm * engy;
fr2y = pref * dbai * (edcy - ebay * cphi[0]) * ctrm * engy;
fr2z = pref * dbai * (edcz - ebaz * cphi[0]) * ctrm * engy;
// Site C
fr3x = pref * ddci * (edcx * cphi[0] - ebax) * ctrm * engy + pref2 * (ddci * (edcx * cphi[c+1] - edfx)) * bptrm * engy;
fr3y = pref * ddci * (edcy * cphi[0] - ebay) * ctrm * engy + pref2 * (ddci * (edcy * cphi[c+1] - edfy)) * bptrm * engy;
fr3z = pref * ddci * (edcz * cphi[0] - ebaz) * ctrm * engy + pref2 * (ddci * (edcz * cphi[c+1] - edfz)) * bptrm * engy;
// Site D
fr4x = pref * ddci * (ebax - edcx * cphi[0]) * ctrm * engy + pref2 * (ddci * (edfx - cphi[c+1] * edcx) + ddfi * (edcx - cphi[c+1] * edfx)) * bptrm * engy + bptrm * ctrm * ddfx * frce;
fr4y = pref * ddci * (ebay - edcy * cphi[0]) * ctrm * engy + pref2 * (ddci * (edfy - cphi[c+1] * edcy) + ddfi * (edcy - cphi[c+1] * edfy)) * bptrm * engy + bptrm * ctrm * ddfy * frce;
fr4z = pref * ddci * (ebaz - edcz * cphi[0]) * ctrm * engy + pref2 * (ddci * (edfz - cphi[c+1] * edcz) + ddfi * (edcz - cphi[c+1] * edfz)) * bptrm * engy + bptrm * ctrm * ddfz * frce;
// Site F
fr5x = pref2 * (ddfi * (edfx * cphi[c+1] - edcx)) * bptrm * engy - bptrm * ctrm * ddfx * frce ;
fr5y = pref2 * (ddfi * (edfy * cphi[c+1] - edcy)) * bptrm * engy - bptrm * ctrm * ddfy * frce ;
fr5z = pref2 * (ddfi * (edfz * cphi[c+1] - edcz)) * bptrm * engy - bptrm * ctrm * ddfz * frce ;
f[stea][0] += fr1x;
f[stea][1] += fr1y;
f[stea][2] += fr1z;
f[steb][0] += fr2x;
f[steb][1] += fr2y;
f[steb][2] += fr2z;
f[stec][0] += fr3x;
f[stec][1] += fr3y;
f[stec][2] += fr3z;
f[sted][0] += fr4x;
f[sted][1] += fr4y;
f[sted][2] += fr4z;
f[stef][0] += fr5x;
f[stef][1] += fr5y;
f[stef][2] += fr5z;
}
else if ((dtha[c+1] > MY_PI/range[c]) || (dtha[c+1] <= -MY_PI/range[c]))
{
}
}
}
return ecstk;
}
/* ---------------------------------------------------------------------- */
double BasePair::base_pairing(double **f)
{
double phi_factor, ftor, ebasepair, first_term, second_term,
cosine, sine, cosine2, sine2, hbon_cosine_term, hbon_cosine_term2;
double prefactor, prefactor2;
double fra1, frb1, frb2, frc1, frc2, frd1;
double fr1x, fr1y, fr1z, fr2x, fr2y, fr2z, fr3x, fr3y, fr3z,
fr4x, fr4y, fr4z, fr5x, fr5y, fr5z, fr6x, fr6y, fr6z;
double frce, engy;
int iphi = 3, itha1 = 4, itha2 = 5, ibp = 2;
ebasepair = 0.0;
phi_factor = 0.5 * (1+cos(dtha[iphi]));
ftor = 0.5 * sin(dtha[iphi]);
// The repulsion is always present
if (ddb < sigm[ibp])
{
mors_rp(ddbsi, alpha[ibp], epsi[ibp], sigm[ibp], &frce, &engy);
ebasepair += engy;
f[steb][0] -= frce * ddbx;
f[steb][1] -= frce * ddby;
f[steb][2] -= frce * ddbz;
f[sted][0] += frce * ddbx;
f[sted][1] += frce * ddby;
f[sted][2] += frce * ddbz;
}
if ( (dtha[itha1] >= -MY_PI/(range[ibp]*2.0)) && (dtha[itha1] <= MY_PI/(range[ibp]*2.0)))
{
if ( (dtha[itha2] >= -MY_PI/(range[ibp]*2.0)) && (dtha[itha2] <= MY_PI/(range[ibp]*2.0)))
{
// Modulated attractive term
mors_norp(ddbsi, alpha[ibp], epsi[ibp], sigm[ibp], &frce, &engy);
ebasepair += phi_factor * engy;
first_term = engy;
second_term = phi_factor * frce;
fra1 = -ftor * dbai * isb2 * first_term;
f[stea][0] += fra1 * padx;
f[stea][1] += fra1 * pady;
f[stea][2] += fra1 * padz;
frb1 = ftor * (ddb - dba * cosb) * dbai * ddbi * isb2 * first_term;
frb2 = ftor * cosd * ddbi * isd2 * first_term;
f[steb][0] += (frb1 * padx + frb2 * pbcx) - second_term * ddbx;
f[steb][1] += (frb1 * pady + frb2 * pbcy) - second_term * ddby;
f[steb][2] += (frb1 * padz + frb2 * pbcz) - second_term * ddbz;
frc1 = ftor * (ddb - ddc * cosd) * ddci * ddbi * isd2 * first_term;
frc2 = ftor * cosb * ddbi * isb2 * first_term;
f[sted][0] += (frc1 * pbcx + frc2 * padx) + second_term * ddbx;
f[sted][1] += (frc1 * pbcy + frc2 * pady) + second_term * ddby;
f[sted][2] += (frc1 * pbcz + frc2 * padz) + second_term * ddbz;
frd1 = -ftor * ddci * isd2 * first_term;
f[stec][0] += frd1 * pbcx;
f[stec][1] += frd1 * pbcy;
f[stec][2] += frd1 * pbcz;
}
else if (((dtha[itha2] >= MY_PI/(range[ibp]*2.0)) && (dtha[itha2] <= MY_PI/range[ibp])) || ((dtha[itha2] <= -MY_PI/(range[ibp]*2.0)) && (dtha[itha2] >= -MY_PI/range[ibp])))
{
// Now I modulated using thata 2
cosine2 = cos(range[ibp]*dtha[itha2]);
sine2 = sin(range[ibp]*dtha[itha2]);
hbon_cosine_term2 = 1.0 - cosine2 * cosine2;
mors_norp(ddbsi, alpha[ibp], epsi[ibp], sigm[ibp], &frce, &engy);
ebasepair += phi_factor * hbon_cosine_term2 * engy;
prefactor2 = 2.0 * range[ibp] * cosine2 * sine2 * 1.0 /sqrt(1.0-cphi[5]*cphi[5]);
// 1 site B
fr1x = prefactor2 * (ddbi * (cphi[5] * edbx - edcx)) * engy - hbon_cosine_term2 * ddbx * frce;
fr1y = prefactor2 * (ddbi * (cphi[5] * edby - edcy)) * engy - hbon_cosine_term2 * ddby * frce;
fr1z = prefactor2 * (ddbi * (cphi[5] * edbz - edcz)) * engy - hbon_cosine_term2 * ddbz * frce;
// 2 site D
fr2x = prefactor2 * (ddci * (edbx - edcx * cphi[5] ) + ddbi * (edcx - cphi[5] * edbx)) * engy + hbon_cosine_term2 * ddbx * frce;
fr2y = prefactor2 * (ddci * (edby - edcy * cphi[5] ) + ddbi * (edcy - cphi[5] * edby)) * engy + hbon_cosine_term2 * ddby * frce;
fr2z = prefactor2 * (ddci * (edbz - edcz * cphi[5] ) + ddbi * (edcz - cphi[5] * edbz)) * engy + hbon_cosine_term2 * ddbz * frce;
// 3 site C
fr3x = prefactor2 * (ddci * (edcx * cphi[5] - edbx)) * engy;
fr3y = prefactor2 * (ddci * (edcy * cphi[5] - edby)) * engy;
fr3z = prefactor2 * (ddci * (edcz * cphi[5] - edbz)) * engy;
f[steb][0] += fr1x * phi_factor;
f[steb][1] += fr1y * phi_factor;
f[steb][2] += fr1z * phi_factor;
f[sted][0] += fr2x * phi_factor;
f[sted][1] += fr2y * phi_factor;
f[sted][2] += fr2z * phi_factor;
f[stec][0] += fr3x * phi_factor;
f[stec][1] += fr3y * phi_factor;
f[stec][2] += fr3z * phi_factor;
first_term = engy * hbon_cosine_term2;
fra1 = -ftor * dbai * isb2 * first_term;
f[stea][0] += fra1 * padx;
f[stea][1] += fra1 * pady;
f[stea][2] += fra1 * padz;
frb1 = ftor * (ddb - dba * cosb) * dbai * ddbi * isb2 * first_term;
frb2 = ftor * cosd * ddbi * isd2 * first_term;
f[steb][0] += (frb1 * padx + frb2 * pbcx);
f[steb][1] += (frb1 * pady + frb2 * pbcy);
f[steb][2] += (frb1 * padz + frb2 * pbcz);
frc1 = ftor * (ddb - ddc * cosd) * ddci * ddbi * isd2 * first_term;
frc2 = ftor * cosb * ddbi * isb2 * first_term;
f[sted][0] += (frc1 * pbcx + frc2 * padx);
f[sted][1] += (frc1 * pbcy + frc2 * pady);
f[sted][2] += (frc1 * pbcz + frc2 * padz);
frd1 = -ftor * ddci * isd2 * first_term;
f[stec][0] += frd1 * pbcx;
f[stec][1] += frd1 * pbcy;
f[stec][2] += frd1 * pbcz;
}
else
{
//f//printf(stdout,"PANIC!: angle difference %lf is outside of permitted range for CS1, %ld, %ld\n",dtha[itha2],stee, steb);
}
}
else if (((dtha[itha1] >= MY_PI/(range[ibp]*2.0)) && (dtha[itha1] <= MY_PI/range[ibp])) || ((dtha[itha1] <= -MY_PI/(range[ibp]*2.0)) && (dtha[itha1] >= -MY_PI/range[ibp])))
{
cosine = cos(range[ibp]*dtha[itha1]);
sine = sin(range[ibp]*dtha[itha1]);
hbon_cosine_term = 1.0 - cosine * cosine;
// Full for dtha[itha2] and modulated dtha1
if ( (dtha[itha2] >= -MY_PI/(range[ibp]*2.0)) && (dtha[itha2] <= MY_PI/(range[ibp]*2.0)))
{
mors_norp(ddbsi, alpha[ibp], epsi[ibp], sigm[ibp], &frce, &engy);
ebasepair += phi_factor * hbon_cosine_term * engy;
prefactor = 2.0 * range[ibp] * cosine * sine * 1.0 /sqrt(1.0-cphi[4]*cphi[4]);
// 1 site A
fr1x = prefactor * (dbai * (cphi[4] * ebax + edbx)) * engy;
fr1y = prefactor * (dbai * (cphi[4] * ebay + edby)) * engy;
fr1z = prefactor * (dbai * (cphi[4] * ebaz + edbz)) * engy;
// 2 site B
fr2x = prefactor * (dbai * (-edbx - ebax * cphi[4] ) + ddbi * (ebax + cphi[4] * edbx)) * engy - hbon_cosine_term * ddbx * frce;
fr2y = prefactor * (dbai * (-edby - ebay * cphi[4] ) + ddbi * (ebay + cphi[4] * edby)) * engy - hbon_cosine_term * ddby * frce;
fr2z = prefactor * (dbai * (-edbz - ebaz * cphi[4] ) + ddbi * (ebaz + cphi[4] * edbz)) * engy - hbon_cosine_term * ddbz * frce;
// 3 site D
fr3x = prefactor * (ddbi * (-edbx * cphi[4] - ebax)) * engy + hbon_cosine_term * ddbx * frce;
fr3y = prefactor * (ddbi * (-edby * cphi[4] - ebay)) * engy + hbon_cosine_term * ddby * frce;
fr3z = prefactor * (ddbi * (-edbz * cphi[4] - ebaz)) * engy + hbon_cosine_term * ddbz * frce;
f[stea][0] += fr1x * phi_factor;
f[stea][1] += fr1y * phi_factor;
f[stea][2] += fr1z * phi_factor;
f[steb][0] += fr2x * phi_factor;
f[steb][1] += fr2y * phi_factor;
f[steb][2] += fr2z * phi_factor;
f[sted][0] += fr3x * phi_factor;
f[sted][1] += fr3y * phi_factor;
f[sted][2] += fr3z * phi_factor;
first_term = engy * hbon_cosine_term;
fra1 = -ftor * dbai * isb2 * first_term;
f[stea][0] += fra1 * padx;
f[stea][1] += fra1 * pady;
f[stea][2] += fra1 * padz;
frb1 = ftor * (ddb - dba * cosb) * dbai * ddbi * isb2 * first_term;
frb2 = ftor * cosd * ddbi * isd2 * first_term;
f[steb][0] += (frb1 * padx + frb2 * pbcx);
f[steb][1] += (frb1 * pady + frb2 * pbcy);
f[steb][2] += (frb1 * padz + frb2 * pbcz);
frc1 = ftor * (ddb - ddc * cosd) * ddci * ddbi * isd2 * first_term;
frc2 = ftor * cosb * ddbi * isb2 * first_term;
f[sted][0] += (frc1 * pbcx + frc2 * padx);
f[sted][1] += (frc1 * pbcy + frc2 * pady);
f[sted][2] += (frc1 * pbcz + frc2 * padz);
frd1 = -ftor * ddci * isd2 * first_term;
f[stec][0] += frd1 * pbcx;
f[stec][1] += frd1 * pbcy;
f[stec][2] += frd1 * pbcz;
}
// Both potentials are modulated
else if (((dtha[itha2] >= MY_PI/(range[ibp]*2.0)) && (dtha[itha2] <= MY_PI/range[ibp])) || ((dtha[itha2] <= -MY_PI/(range[ibp]*2.0)) && (dtha[itha2] >= -MY_PI/range[ibp])))
{
cosine2 = cos(range[ibp]*dtha[itha2]);
sine2 = sin(range[ibp]*dtha[itha2]);
hbon_cosine_term2 = 1.0 - cosine2 * cosine2;
mors_norp(ddbsi, alpha[ibp], epsi[ibp], sigm[ibp], &frce, &engy);
ebasepair += phi_factor * hbon_cosine_term * hbon_cosine_term2 * engy;
prefactor2 = 2.0 * range[ibp] * cosine2 * sine2 * 1.0 /sqrt(1.0-cphi[5]*cphi[5]);
prefactor = 2.0 * range[ibp] * cosine * sine * 1.0 /sqrt(1.0-cphi[4]*cphi[4]);
// Site A
fr1x = prefactor * (dbai * (cphi[4] * ebax + edbx)) * hbon_cosine_term2 * engy;
fr1y = prefactor * (dbai * (cphi[4] * ebay + edby)) * hbon_cosine_term2 * engy;
fr1z = prefactor * (dbai * (cphi[4] * ebaz + edbz)) * hbon_cosine_term2 * engy;
// Site B
fr2x = prefactor * (dbai * (-edbx - ebax * cphi[4] ) + ddbi * (ebax + cphi[4] * edbx)) * hbon_cosine_term2 * engy + prefactor2 * (ddbi * (cphi[5] * edbx - edcx)) * hbon_cosine_term * engy - hbon_cosine_term * hbon_cosine_term2 * ddbx * frce;
fr2y = prefactor * (dbai * (-edby - ebay * cphi[4] ) + ddbi * (ebay + cphi[4] * edby)) * hbon_cosine_term2 * engy + prefactor2 * (ddbi * (cphi[5] * edby - edcy)) * hbon_cosine_term * engy - hbon_cosine_term * hbon_cosine_term2 * ddby * frce;
fr2z = prefactor * (dbai * (-edbz - ebaz * cphi[4] ) + ddbi * (ebaz + cphi[4] * edbz)) * hbon_cosine_term2 * engy + prefactor2 * (ddbi * (cphi[5] * edbz - edcz)) * hbon_cosine_term * engy - hbon_cosine_term * hbon_cosine_term2 * ddbz * frce;
// Site C
fr3x = prefactor2 * (ddci * (edcx * cphi[5] - edbx)) * hbon_cosine_term * engy;
fr3y = prefactor2 * (ddci * (edcy * cphi[5] - edby)) * hbon_cosine_term * engy;
fr3z = prefactor2 * (ddci * (edcz * cphi[5] - edbz)) * hbon_cosine_term * engy;
// Site D
fr4x = prefactor * (ddbi * (-edbx * cphi[4] - ebax)) * hbon_cosine_term2 * engy + prefactor2 * (ddci * (edbx - edcx * cphi[5] ) + ddbi * (edcx - cphi[5] * edbx)) * hbon_cosine_term * engy + hbon_cosine_term * hbon_cosine_term2 * ddbx * frce;
fr4y = prefactor * (ddbi * (-edby * cphi[4] - ebay)) * hbon_cosine_term2 * engy + prefactor2 * (ddci * (edby - edcy * cphi[5] ) + ddbi * (edcy - cphi[5] * edby)) * hbon_cosine_term * engy + hbon_cosine_term * hbon_cosine_term2 * ddby * frce;
fr4z = prefactor * (ddbi * (-edbz * cphi[4] - ebaz)) * hbon_cosine_term2 * engy + prefactor2 * (ddci * (edbz - edcz * cphi[5] ) + ddbi * (edcz - cphi[5] * edbz)) * hbon_cosine_term * engy + hbon_cosine_term * hbon_cosine_term2 * ddbz * frce;
f[stea][0] += fr1x * phi_factor;
f[stea][1] += fr1y * phi_factor;
f[stea][2] += fr1z * phi_factor;
f[steb][0] += fr2x * phi_factor;
f[steb][1] += fr2y * phi_factor;
f[steb][2] += fr2z * phi_factor;
f[stec][0] += fr3x * phi_factor;
f[stec][1] += fr3y * phi_factor;
f[stec][2] += fr3z * phi_factor;
f[sted][0] += fr4x * phi_factor;
f[sted][1] += fr4y * phi_factor;
f[sted][2] += fr4z * phi_factor;
// Code block
first_term = engy * hbon_cosine_term * hbon_cosine_term2;
fra1 = -ftor * dbai * isb2 * first_term;
f[stea][0] += fra1 * padx;
f[stea][1] += fra1 * pady;
f[stea][2] += fra1 * padz;
frb1 = ftor * (ddb - dba * cosb) * dbai * ddbi * isb2 * first_term;
frb2 = ftor * cosd * ddbi * isd2 * first_term;
f[steb][0] += (frb1 * padx + frb2 * pbcx);
f[steb][1] += (frb1 * pady + frb2 * pbcy);
f[steb][2] += (frb1 * padz + frb2 * pbcz);
frc1 = ftor * (ddb - ddc * cosd) * ddci * ddbi * isd2 * first_term;
frc2 = ftor * cosb * ddbi * isb2 * first_term;
f[sted][0] += (frc1 * pbcx + frc2 * padx);
f[sted][1] += (frc1 * pbcy + frc2 * pady);
f[sted][2] += (frc1 * pbcz + frc2 * padz);
frd1 = -ftor * ddci * isd2 * first_term;
f[stec][0] += frd1 * pbcx;
f[stec][1] += frd1 * pbcy;
f[stec][2] += frd1 * pbcz;
}
else
{
}
}
else if ((dtha[itha1] >= MY_PI/range[ibp]) || (dtha[itha1] <= -MY_PI/range[ibp]))
{
}
else
{
}
// Now return total energy of interaction
return ebasepair;
}
/* ---------------------------------------------------------------------- */
void BasePair::mors_norp( double drsi, double alfa, double epsi, double sigm,
double *forc, double *ener)
{
double disi, dist, argu;
disi = sqrt(drsi);
dist = 1.0 / disi;
if (dist > sigm)
{
argu = alfa * (dist - sigm);
*ener = epsi * (1.0 - exp(-argu)) * (1.0 - exp(-argu)) - epsi;
*forc =
-2.0 * alfa * epsi * disi * exp(-argu) * (1.0 - exp(-argu));
}
else
{
*ener = -epsi;
*forc = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void BasePair::mors_rp(double drsi, double alfa, double epsi, double sigm,
double *forc, double *ener)
{
double disi, dist, argu;
disi = sqrt(drsi);
dist = 1.0 / disi;
if (dist < sigm)
{
argu = alfa * (dist - sigm);
*ener = epsi * (1.0 - exp(-argu)) * (1.0 - exp(-argu));
*forc =
-2.0 * alfa * epsi * disi * exp(-argu) * (1.0 - exp(-argu));
}
else
{
*ener = 0.0;
*forc = 0.0;
}
}