1 |
#include "primitives/Torsion.hpp"
|
2 |
|
3 |
namespace oopse {
|
4 |
|
5 |
Torsion::Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt)
|
6 |
: atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4) {
|
7 |
|
8 |
}
|
9 |
|
10 |
void Torsion::calcForce() {
|
11 |
|
12 |
Vector3d pos1 = atom1_->getPos();
|
13 |
Vector3d pos2 = atom2_->getPos();
|
14 |
Vector3d pos3 = atom3_->getPos();
|
15 |
Vector3d pos4 = atom4_->getPos();
|
16 |
|
17 |
Vector3d r12 = pos1 - pos2;
|
18 |
Vector3d r23 = pos2 - pos3;
|
19 |
Vector3d r34 = pos3 - pos4;
|
20 |
|
21 |
// Calculate the cross products and distances
|
22 |
Vector3d A = cross(r12,r23);
|
23 |
double rA = A.length();
|
24 |
Vector3d B = cross(r23,r34);
|
25 |
double rB = B.length();
|
26 |
Vector3d C = cross(r23,A);
|
27 |
double rC = C.length();
|
28 |
|
29 |
// Calculate the sin and cos
|
30 |
double cos_phi = (A*B)/(rA*rB);
|
31 |
double sin_phi = (C*B)/(rC*rB);
|
32 |
|
33 |
double phi= -atan2(sin_phi,cos_phi);
|
34 |
|
35 |
double firstDerivative;
|
36 |
torsionType_->calcForce(phi, firstDerivative, potential_);
|
37 |
|
38 |
|
39 |
Vector3d f1,f2,f3;
|
40 |
|
41 |
// Normalize B
|
42 |
rB = 1.0/rB;
|
43 |
B *= rB;
|
44 |
|
45 |
// Next, we want to calculate the forces. In order
|
46 |
// to do that, we first need to figure out whether the
|
47 |
// sin or cos form will be more stable. For this,
|
48 |
// just look at the value of phi
|
49 |
if (fabs(sin_phi) > 0.1) {
|
50 |
// use the sin version to avoid 1/cos terms
|
51 |
|
52 |
rA = 1.0/rA;
|
53 |
A *= rA;
|
54 |
Vector3d dcosdA = rA*(cos_phi*A-B);
|
55 |
Vector3d dcosdB = rB*(cos_phi*B-A);
|
56 |
|
57 |
K1 = K1/sin_phi;
|
58 |
|
59 |
//simple form
|
60 |
//f1 = K1 * cross(r23, dcosdA);
|
61 |
//f3 = K1 * cross(r23, dcosdB);
|
62 |
//f2 = K1 * ( cross(r34, dcosdB) - cross(r12, dcosdA));
|
63 |
|
64 |
f1.x = K1*(r23.y*dcosdA.z - r23.z*dcosdA.y);
|
65 |
f1.y = K1*(r23.z*dcosdA.x - r23.x*dcosdA.z);
|
66 |
f1.z = K1*(r23.x*dcosdA.y - r23.y*dcosdA.x);
|
67 |
|
68 |
f3.x = K1*(r23.z*dcosdB.y - r23.y*dcosdB.z);
|
69 |
f3.y = K1*(r23.x*dcosdB.z - r23.z*dcosdB.x);
|
70 |
f3.z = K1*(r23.y*dcosdB.x - r23.x*dcosdB.y);
|
71 |
|
72 |
f2.x = K1*(r12.z*dcosdA.y - r12.y*dcosdA.z + r34.y*dcosdB.z - r34.z*dcosdB.y);
|
73 |
f2.y = K1*(r12.x*dcosdA.z - r12.z*dcosdA.x + r34.z*dcosdB.x - r34.x*dcosdB.z);
|
74 |
f2.z = K1*(r12.y*dcosdA.x - r12.x*dcosdA.y + r34.x*dcosdB.y - r34.y*dcosdB.x);
|
75 |
} else {
|
76 |
// This angle is closer to 0 or 180 than it is to
|
77 |
// 90, so use the cos version to avoid 1/sin terms
|
78 |
|
79 |
// Normalize C
|
80 |
rC = 1.0/rC;
|
81 |
C *= rC;
|
82 |
Vector3d dsindC = rC*(sin_phi*C-B);
|
83 |
Vector3d dsindB = rB*(sin_phi*B-C);
|
84 |
|
85 |
K1 = -K1/cos_phi;
|
86 |
|
87 |
f1.x = K1*((r23.y*r23.y + r23.z*r23.z)*dsindC.x - r23.x*r23.y*dsindC.y - r23.x*r23.z*dsindC.z);
|
88 |
f1.y = K1*((r23.z*r23.z + r23.x*r23.x)*dsindC.y - r23.y*r23.z*dsindC.z - r23.y*r23.x*dsindC.x);
|
89 |
f1.z = K1*((r23.x*r23.x + r23.y*r23.y)*dsindC.z - r23.z*r23.x*dsindC.x - r23.z*r23.y*dsindC.y);
|
90 |
|
91 |
f3 = K1 *cross(dsindB,r23);
|
92 |
|
93 |
f2.x = K1*(-(r23.y*r12.y + r23.z*r12.z)*dsindC.x + (2.0*r23.x*r12.y - r12.x*r23.y)*dsindC.y
|
94 |
+ (2.0*r23.x*r12.z - r12.x*r23.z)*dsindC.z + dsindB.z*r34.y - dsindB.y*r34.z);
|
95 |
f2.y = K1*(-(r23.z*r12.z + r23.x*r12.x)*dsindC.y + (2.0*r23.y*r12.z - r12.y*r23.z)*dsindC.z
|
96 |
+ (2.0*r23.y*r12.x - r12.y*r23.x)*dsindC.x + dsindB.x*r34.z - dsindB.z*r34.x);
|
97 |
f2.z = K1*(-(r23.x*r12.x + r23.y*r12.y)*dsindC.z + (2.0*r23.z*r12.x - r12.z*r23.x)*dsindC.x
|
98 |
+(2.0*r23.z*r12.y - r12.z*r23.y)*dsindC.y + dsindB.y*r34.x - dsindB.x*r34.y);
|
99 |
}
|
100 |
|
101 |
atom1_->addFrc(f1);
|
102 |
atom2_->addFrc(f2 - f1);
|
103 |
atom3_->addFrc(f3 - f2);
|
104 |
atom4_->addFrc(-f3);
|
105 |
|
106 |
}
|
107 |
|
108 |
|
109 |
double K=0; // energy
|
110 |
double K1=0; // force
|
111 |
|
112 |
// get the dihedral information
|
113 |
int multiplicity = value->multiplicity;
|
114 |
|
115 |
// Loop through the multiple parameter sets for this
|
116 |
// bond. We will only loop more than once if this
|
117 |
// has multiple parameter sets from Charmm22
|
118 |
for (int mult_num=0; mult_num<multiplicity; mult_num++)
|
119 |
{
|
120 |
/* get angle information */
|
121 |
double k = value->values[mult_num].k * scale;
|
122 |
double delta = value->values[mult_num].delta;
|
123 |
int n = value->values[mult_num].n;
|
124 |
|
125 |
// Calculate the energy
|
126 |
if (n)
|
127 |
{
|
128 |
// Periodicity is greater than 0, so use cos form
|
129 |
K += k*(1+cos(n*phi + delta));
|
130 |
K1 += -n*k*sin(n*phi + delta);
|
131 |
}
|
132 |
else
|
133 |
{
|
134 |
// Periodicity is 0, so just use the harmonic form
|
135 |
double diff = phi-delta;
|
136 |
if (diff < -PI) diff += TWOPI;
|
137 |
else if (diff > PI) diff -= TWOPI;
|
138 |
|
139 |
K += k*diff*diff;
|
140 |
K1 += 2.0*k*diff;
|
141 |
}
|
142 |
} /* for multiplicity */
|
143 |
|
144 |
|
145 |
void Torsion::calc_forces(){
|
146 |
|
147 |
/**********************************************************************
|
148 |
*
|
149 |
* initialize vectors
|
150 |
*
|
151 |
***********************************************************************/
|
152 |
|
153 |
vect r_ab; /* the vector whose origin is a and end is b */
|
154 |
vect r_cb; /* the vector whose origin is c and end is b */
|
155 |
vect r_cd; /* the vector whose origin is c and end is b */
|
156 |
vect r_cr1; /* the cross product of r_ab and r_cb */
|
157 |
vect r_cr2; /* the cross product of r_cb and r_cd */
|
158 |
|
159 |
double r_cr1_x2; /* the components of r_cr1 squared */
|
160 |
double r_cr1_y2;
|
161 |
double r_cr1_z2;
|
162 |
|
163 |
double r_cr2_x2; /* the components of r_cr2 squared */
|
164 |
double r_cr2_y2;
|
165 |
double r_cr2_z2;
|
166 |
|
167 |
double r_cr1_sqr; /* the length of r_cr1 squared */
|
168 |
double r_cr2_sqr; /* the length of r_cr2 squared */
|
169 |
|
170 |
double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */
|
171 |
|
172 |
Vector3d aR, bR, cR, dR;
|
173 |
Vector3d aF, bF, cF, dF;
|
174 |
|
175 |
aR = c_p_a->getPos();
|
176 |
bR = c_p_b->getPos();
|
177 |
cR = c_p_c->getPos();
|
178 |
dR = c_p_d->getPos();
|
179 |
|
180 |
r_ab.x = bR[0] - aR[0];
|
181 |
r_ab.y = bR[1] - aR[1];
|
182 |
r_ab.z = bR[2] - aR[2];
|
183 |
r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z));
|
184 |
|
185 |
r_cb.x = bR[0] - cR[0];
|
186 |
r_cb.y = bR[1] - cR[1];
|
187 |
r_cb.z = bR[2] - cR[2];
|
188 |
r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z));
|
189 |
|
190 |
r_cd.x = dR[0] - cR[0];
|
191 |
r_cd.y = dR[1] - cR[1];
|
192 |
r_cd.z = dR[2] - cR[2];
|
193 |
r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z));
|
194 |
|
195 |
r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z;
|
196 |
r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x;
|
197 |
r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y;
|
198 |
r_cr1_x2 = r_cr1.x * r_cr1.x;
|
199 |
r_cr1_y2 = r_cr1.y * r_cr1.y;
|
200 |
r_cr1_z2 = r_cr1.z * r_cr1.z;
|
201 |
r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2;
|
202 |
r_cr1.length = sqrt(r_cr1_sqr);
|
203 |
|
204 |
r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z;
|
205 |
r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x;
|
206 |
r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y;
|
207 |
r_cr2_x2 = r_cr2.x * r_cr2.x;
|
208 |
r_cr2_y2 = r_cr2.y * r_cr2.y;
|
209 |
r_cr2_z2 = r_cr2.z * r_cr2.z;
|
210 |
r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2;
|
211 |
r_cr2.length = sqrt(r_cr2_sqr);
|
212 |
|
213 |
r_cr1_r_cr2 = r_cr1.length * r_cr2.length;
|
214 |
|
215 |
//Vector3d pos1 = atom1_->getPos();
|
216 |
//Vector3d pos2 = atom2_->getPos();
|
217 |
//Vector3d pos3 = atom3_->getPos();
|
218 |
//Vector3d pos4 = atom4_->getPos();
|
219 |
|
220 |
//Vector3d r12 = pos2 - pos1;
|
221 |
//Vector3d r32 = pos2 - pos3;
|
222 |
//Vector3d r34 = pos4 - pos3;
|
223 |
|
224 |
//A = cross(r12, r32);
|
225 |
//B = cross(r32, r34);
|
226 |
|
227 |
//rA = A.length();
|
228 |
//rB = B.length();
|
229 |
|
230 |
/**********************************************************************
|
231 |
*
|
232 |
* dot product and angle calculations
|
233 |
*
|
234 |
***********************************************************************/
|
235 |
|
236 |
double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */
|
237 |
double cos_phi; /* the cosine of the torsion angle */
|
238 |
|
239 |
cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z;
|
240 |
|
241 |
cos_phi = cr1_dot_cr2 / r_cr1_r_cr2;
|
242 |
|
243 |
/* adjust for the granularity of the numbers for angles near 0 or pi */
|
244 |
|
245 |
if(cos_phi > 1.0) cos_phi = 1.0;
|
246 |
if(cos_phi < -1.0) cos_phi = -1.0;
|
247 |
|
248 |
//cos_phi = dot (A, B) / (rA * rB);
|
249 |
//if (cos_phi > 1.0) {
|
250 |
// cos_phi = 1.0;
|
251 |
//}
|
252 |
//if (cos_phi < -1.0) {
|
253 |
// cos_phi = -1.0;
|
254 |
//}
|
255 |
|
256 |
|
257 |
|
258 |
/********************************************************************
|
259 |
*
|
260 |
* This next section calculates derivatives needed for the force
|
261 |
* calculation
|
262 |
*
|
263 |
********************************************************************/
|
264 |
|
265 |
|
266 |
/* the derivatives of cos phi with respect to the x, y,
|
267 |
and z components of vectors cr1 and cr2. */
|
268 |
double d_cos_dx_cr1;
|
269 |
double d_cos_dy_cr1;
|
270 |
double d_cos_dz_cr1;
|
271 |
double d_cos_dx_cr2;
|
272 |
double d_cos_dy_cr2;
|
273 |
double d_cos_dz_cr2;
|
274 |
|
275 |
d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr;
|
276 |
d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr;
|
277 |
d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr;
|
278 |
|
279 |
d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr;
|
280 |
d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr;
|
281 |
d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr;
|
282 |
|
283 |
//Vector3d dcosdA = B /(rA * rB) - cos_phi /(rA * rA) * A;
|
284 |
//Vector3d dcosdA = 1.0 /rA * (B.normalize() - cos_phi * A.normalize());
|
285 |
//Vector3d dcosdB = 1.0 /rB * (A.normalize() - cos_phi * B.normalize());
|
286 |
|
287 |
/***********************************************************************
|
288 |
*
|
289 |
* Calculate the actual forces and place them in the atoms.
|
290 |
*
|
291 |
***********************************************************************/
|
292 |
|
293 |
double force; /*the force scaling factor */
|
294 |
|
295 |
force = torsion_force(cos_phi);
|
296 |
|
297 |
aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y);
|
298 |
aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z);
|
299 |
aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x);
|
300 |
|
301 |
bF[0] = force * ( d_cos_dy_cr1 * (r_ab.z - r_cb.z)
|
302 |
- d_cos_dy_cr2 * r_cd.z
|
303 |
+ d_cos_dz_cr1 * (r_cb.y - r_ab.y)
|
304 |
+ d_cos_dz_cr2 * r_cd.y);
|
305 |
bF[1] = force * ( d_cos_dx_cr1 * (r_cb.z - r_ab.z)
|
306 |
+ d_cos_dx_cr2 * r_cd.z
|
307 |
+ d_cos_dz_cr1 * (r_ab.x - r_cb.x)
|
308 |
- d_cos_dz_cr2 * r_cd.x);
|
309 |
bF[2] = force * ( d_cos_dx_cr1 * (r_ab.y - r_cb.y)
|
310 |
- d_cos_dx_cr2 * r_cd.y
|
311 |
+ d_cos_dy_cr1 * (r_cb.x - r_ab.x)
|
312 |
+ d_cos_dy_cr2 * r_cd.x);
|
313 |
|
314 |
cF[0] = force * (- d_cos_dy_cr1 * r_ab.z
|
315 |
- d_cos_dy_cr2 * (r_cb.z - r_cd.z)
|
316 |
+ d_cos_dz_cr1 * r_ab.y
|
317 |
- d_cos_dz_cr2 * (r_cd.y - r_cb.y));
|
318 |
cF[1] = force * ( d_cos_dx_cr1 * r_ab.z
|
319 |
- d_cos_dx_cr2 * (r_cd.z - r_cb.z)
|
320 |
- d_cos_dz_cr1 * r_ab.x
|
321 |
- d_cos_dz_cr2 * (r_cb.x - r_cd.x));
|
322 |
cF[2] = force * (- d_cos_dx_cr1 * r_ab.y
|
323 |
- d_cos_dx_cr2 * (r_cb.y - r_cd.y)
|
324 |
+ d_cos_dy_cr1 * r_ab.x
|
325 |
- d_cos_dy_cr2 * (r_cd.x - r_cb.x));
|
326 |
|
327 |
dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y);
|
328 |
dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z);
|
329 |
dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x);
|
330 |
|
331 |
|
332 |
c_p_a->addFrc(aF);
|
333 |
c_p_b->addFrc(bF);
|
334 |
c_p_c->addFrc(cF);
|
335 |
c_p_d->addFrc(dF);
|
336 |
|
337 |
//double firstDerivative;
|
338 |
//bondType_->calcForce(cos_phi, firstDerivative, potential_);
|
339 |
//f1 = force * cross (dcosdA, r32);
|
340 |
//f2 =
|
341 |
//f3 =
|
342 |
//f4 = force * cross(dcosdB, r32);
|
343 |
//atom1_->addFrc(f1);
|
344 |
//atom2_->addFrc(f2);
|
345 |
//atom3_->addFrc(f3);
|
346 |
//atom4_->addFrc(f4);
|
347 |
|
348 |
|
349 |
}
|
350 |
|
351 |
}
|