1 |
– |
<<<<<<< Torsion.cpp |
1 |
|
#include "primitives/Torsion.hpp" |
2 |
|
|
3 |
|
namespace oopse { |
4 |
|
|
6 |
– |
Torsion::Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt) |
7 |
– |
: atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4) { |
8 |
– |
|
9 |
– |
} |
10 |
– |
|
11 |
– |
void Torsion::calcForce() { |
12 |
– |
|
13 |
– |
Vector3d pos1 = atom1_->getPos(); |
14 |
– |
Vector3d pos2 = atom2_->getPos(); |
15 |
– |
Vector3d pos3 = atom3_->getPos(); |
16 |
– |
Vector3d pos4 = atom4_->getPos(); |
17 |
– |
|
18 |
– |
Vector3d r12 = pos1 - pos2; |
19 |
– |
Vector3d r23 = pos2 - pos3; |
20 |
– |
Vector3d r34 = pos3 - pos4; |
21 |
– |
|
22 |
– |
// Calculate the cross products and distances |
23 |
– |
Vector3d A = cross(r12,r23); |
24 |
– |
double rA = A.length(); |
25 |
– |
Vector3d B = cross(r23,r34); |
26 |
– |
double rB = B.length(); |
27 |
– |
Vector3d C = cross(r23,A); |
28 |
– |
double rC = C.length(); |
29 |
– |
|
30 |
– |
// Calculate the sin and cos |
31 |
– |
double cos_phi = (A*B)/(rA*rB); |
32 |
– |
double sin_phi = (C*B)/(rC*rB); |
33 |
– |
|
34 |
– |
double phi= -atan2(sin_phi,cos_phi); |
35 |
– |
|
36 |
– |
double firstDerivative; |
37 |
– |
|
38 |
– |
torsionType_->calcForce(cosPhi, sinPhi, Vtorsion, dVdCosPhi); |
39 |
– |
|
40 |
– |
|
41 |
– |
Vector3d f1,f2,f3; |
42 |
– |
|
43 |
– |
// Normalize B |
44 |
– |
rB = 1.0/rB; |
45 |
– |
B *= rB; |
46 |
– |
|
47 |
– |
// Next, we want to calculate the forces. In order |
48 |
– |
// to do that, we first need to figure out whether the |
49 |
– |
// sin or cos form will be more stable. For this, |
50 |
– |
// just look at the value of phi |
51 |
– |
if (fabs(sin_phi) > 0.1) { |
52 |
– |
// use the sin version to avoid 1/cos terms |
53 |
– |
|
54 |
– |
rA = 1.0/rA; |
55 |
– |
A *= rA; |
56 |
– |
Vector3d dcosdA = rA*(cos_phi*A-B); |
57 |
– |
Vector3d dcosdB = rB*(cos_phi*B-A); |
58 |
– |
|
59 |
– |
K1 = K1/sin_phi; |
60 |
– |
|
61 |
– |
//simple form |
62 |
– |
//f1 = K1 * cross(r23, dcosdA); |
63 |
– |
//f3 = K1 * cross(r23, dcosdB); |
64 |
– |
//f2 = K1 * ( cross(r34, dcosdB) - cross(r12, dcosdA)); |
65 |
– |
|
66 |
– |
f1.x = K1*(r23.y*dcosdA.z - r23.z*dcosdA.y); |
67 |
– |
f1.y = K1*(r23.z*dcosdA.x - r23.x*dcosdA.z); |
68 |
– |
f1.z = K1*(r23.x*dcosdA.y - r23.y*dcosdA.x); |
69 |
– |
|
70 |
– |
f3.x = K1*(r23.z*dcosdB.y - r23.y*dcosdB.z); |
71 |
– |
f3.y = K1*(r23.x*dcosdB.z - r23.z*dcosdB.x); |
72 |
– |
f3.z = K1*(r23.y*dcosdB.x - r23.x*dcosdB.y); |
73 |
– |
|
74 |
– |
f2.x = K1*(r12.z*dcosdA.y - r12.y*dcosdA.z + r34.y*dcosdB.z - r34.z*dcosdB.y); |
75 |
– |
f2.y = K1*(r12.x*dcosdA.z - r12.z*dcosdA.x + r34.z*dcosdB.x - r34.x*dcosdB.z); |
76 |
– |
f2.z = K1*(r12.y*dcosdA.x - r12.x*dcosdA.y + r34.x*dcosdB.y - r34.y*dcosdB.x); |
77 |
– |
} else { |
78 |
– |
// This angle is closer to 0 or 180 than it is to |
79 |
– |
// 90, so use the cos version to avoid 1/sin terms |
80 |
– |
|
81 |
– |
// Normalize C |
82 |
– |
rC = 1.0/rC; |
83 |
– |
C *= rC; |
84 |
– |
Vector3d dsindC = rC*(sin_phi*C-B); |
85 |
– |
Vector3d dsindB = rB*(sin_phi*B-C); |
86 |
– |
|
87 |
– |
K1 = -K1/cos_phi; |
88 |
– |
|
89 |
– |
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); |
90 |
– |
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); |
91 |
– |
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); |
92 |
– |
|
93 |
– |
f3 = K1 *cross(dsindB,r23); |
94 |
– |
|
95 |
– |
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 |
96 |
– |
+ (2.0*r23.x*r12.z - r12.x*r23.z)*dsindC.z + dsindB.z*r34.y - dsindB.y*r34.z); |
97 |
– |
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 |
98 |
– |
+ (2.0*r23.y*r12.x - r12.y*r23.x)*dsindC.x + dsindB.x*r34.z - dsindB.z*r34.x); |
99 |
– |
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 |
100 |
– |
+(2.0*r23.z*r12.y - r12.z*r23.y)*dsindC.y + dsindB.y*r34.x - dsindB.x*r34.y); |
101 |
– |
} |
102 |
– |
|
103 |
– |
atom1_->addFrc(f1); |
104 |
– |
atom2_->addFrc(f2 - f1); |
105 |
– |
atom3_->addFrc(f3 - f2); |
106 |
– |
atom4_->addFrc(-f3); |
107 |
– |
|
108 |
– |
} |
109 |
– |
|
110 |
– |
|
111 |
– |
double K=0; // energy |
112 |
– |
double K1=0; // force |
113 |
– |
|
114 |
– |
// get the dihedral information |
115 |
– |
int multiplicity = value->multiplicity; |
116 |
– |
|
117 |
– |
// Loop through the multiple parameter sets for this |
118 |
– |
// bond. We will only loop more than once if this |
119 |
– |
// has multiple parameter sets from Charmm22 |
120 |
– |
for (int mult_num=0; mult_num<multiplicity; mult_num++) |
121 |
– |
{ |
122 |
– |
/* get angle information */ |
123 |
– |
double k = value->values[mult_num].k * scale; |
124 |
– |
double delta = value->values[mult_num].delta; |
125 |
– |
int n = value->values[mult_num].n; |
126 |
– |
|
127 |
– |
// Calculate the energy |
128 |
– |
if (n) |
129 |
– |
{ |
130 |
– |
// Periodicity is greater than 0, so use cos form |
131 |
– |
K += k*(1+cos(n*phi + delta)); |
132 |
– |
K1 += -n*k*sin(n*phi + delta); |
133 |
– |
} |
134 |
– |
else |
135 |
– |
{ |
136 |
– |
// Periodicity is 0, so just use the harmonic form |
137 |
– |
double diff = phi-delta; |
138 |
– |
if (diff < -PI) diff += TWOPI; |
139 |
– |
else if (diff > PI) diff -= TWOPI; |
140 |
– |
|
141 |
– |
K += k*diff*diff; |
142 |
– |
K1 += 2.0*k*diff; |
143 |
– |
} |
144 |
– |
} /* for multiplicity */ |
145 |
– |
|
146 |
– |
|
147 |
– |
void Torsion::calc_forces(){ |
148 |
– |
|
149 |
– |
/********************************************************************** |
150 |
– |
* |
151 |
– |
* initialize vectors |
152 |
– |
* |
153 |
– |
***********************************************************************/ |
154 |
– |
|
155 |
– |
vect r_ab; /* the vector whose origin is a and end is b */ |
156 |
– |
vect r_cb; /* the vector whose origin is c and end is b */ |
157 |
– |
vect r_cd; /* the vector whose origin is c and end is b */ |
158 |
– |
vect r_cr1; /* the cross product of r_ab and r_cb */ |
159 |
– |
vect r_cr2; /* the cross product of r_cb and r_cd */ |
160 |
– |
|
161 |
– |
double r_cr1_x2; /* the components of r_cr1 squared */ |
162 |
– |
double r_cr1_y2; |
163 |
– |
double r_cr1_z2; |
164 |
– |
|
165 |
– |
double r_cr2_x2; /* the components of r_cr2 squared */ |
166 |
– |
double r_cr2_y2; |
167 |
– |
double r_cr2_z2; |
168 |
– |
|
169 |
– |
double r_cr1_sqr; /* the length of r_cr1 squared */ |
170 |
– |
double r_cr2_sqr; /* the length of r_cr2 squared */ |
171 |
– |
|
172 |
– |
double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */ |
173 |
– |
|
174 |
– |
Vector3d aR, bR, cR, dR; |
175 |
– |
Vector3d aF, bF, cF, dF; |
176 |
– |
|
177 |
– |
aR = c_p_a->getPos(); |
178 |
– |
bR = c_p_b->getPos(); |
179 |
– |
cR = c_p_c->getPos(); |
180 |
– |
dR = c_p_d->getPos(); |
181 |
– |
|
182 |
– |
r_ab.x = bR[0] - aR[0]; |
183 |
– |
r_ab.y = bR[1] - aR[1]; |
184 |
– |
r_ab.z = bR[2] - aR[2]; |
185 |
– |
r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z)); |
186 |
– |
|
187 |
– |
r_cb.x = bR[0] - cR[0]; |
188 |
– |
r_cb.y = bR[1] - cR[1]; |
189 |
– |
r_cb.z = bR[2] - cR[2]; |
190 |
– |
r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z)); |
191 |
– |
|
192 |
– |
r_cd.x = dR[0] - cR[0]; |
193 |
– |
r_cd.y = dR[1] - cR[1]; |
194 |
– |
r_cd.z = dR[2] - cR[2]; |
195 |
– |
r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z)); |
196 |
– |
|
197 |
– |
r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z; |
198 |
– |
r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x; |
199 |
– |
r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y; |
200 |
– |
r_cr1_x2 = r_cr1.x * r_cr1.x; |
201 |
– |
r_cr1_y2 = r_cr1.y * r_cr1.y; |
202 |
– |
r_cr1_z2 = r_cr1.z * r_cr1.z; |
203 |
– |
r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2; |
204 |
– |
r_cr1.length = sqrt(r_cr1_sqr); |
205 |
– |
|
206 |
– |
r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z; |
207 |
– |
r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x; |
208 |
– |
r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y; |
209 |
– |
r_cr2_x2 = r_cr2.x * r_cr2.x; |
210 |
– |
r_cr2_y2 = r_cr2.y * r_cr2.y; |
211 |
– |
r_cr2_z2 = r_cr2.z * r_cr2.z; |
212 |
– |
r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2; |
213 |
– |
r_cr2.length = sqrt(r_cr2_sqr); |
214 |
– |
|
215 |
– |
r_cr1_r_cr2 = r_cr1.length * r_cr2.length; |
216 |
– |
|
217 |
– |
//Vector3d pos1 = atom1_->getPos(); |
218 |
– |
//Vector3d pos2 = atom2_->getPos(); |
219 |
– |
//Vector3d pos3 = atom3_->getPos(); |
220 |
– |
//Vector3d pos4 = atom4_->getPos(); |
221 |
– |
|
222 |
– |
//Vector3d r12 = pos2 - pos1; |
223 |
– |
//Vector3d r32 = pos2 - pos3; |
224 |
– |
//Vector3d r34 = pos4 - pos3; |
225 |
– |
|
226 |
– |
//A = cross(r12, r32); |
227 |
– |
//B = cross(r32, r34); |
228 |
– |
|
229 |
– |
//rA = A.length(); |
230 |
– |
//rB = B.length(); |
231 |
– |
|
232 |
– |
/********************************************************************** |
233 |
– |
* |
234 |
– |
* dot product and angle calculations |
235 |
– |
* |
236 |
– |
***********************************************************************/ |
237 |
– |
|
238 |
– |
double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */ |
239 |
– |
double cos_phi; /* the cosine of the torsion angle */ |
240 |
– |
|
241 |
– |
cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z; |
242 |
– |
|
243 |
– |
cos_phi = cr1_dot_cr2 / r_cr1_r_cr2; |
244 |
– |
|
245 |
– |
/* adjust for the granularity of the numbers for angles near 0 or pi */ |
246 |
– |
|
247 |
– |
if(cos_phi > 1.0) cos_phi = 1.0; |
248 |
– |
if(cos_phi < -1.0) cos_phi = -1.0; |
249 |
– |
|
250 |
– |
//cos_phi = dot (A, B) / (rA * rB); |
251 |
– |
//if (cos_phi > 1.0) { |
252 |
– |
// cos_phi = 1.0; |
253 |
– |
//} |
254 |
– |
//if (cos_phi < -1.0) { |
255 |
– |
// cos_phi = -1.0; |
256 |
– |
//} |
257 |
– |
|
258 |
– |
|
259 |
– |
|
260 |
– |
/******************************************************************** |
261 |
– |
* |
262 |
– |
* This next section calculates derivatives needed for the force |
263 |
– |
* calculation |
264 |
– |
* |
265 |
– |
********************************************************************/ |
266 |
– |
|
267 |
– |
|
268 |
– |
/* the derivatives of cos phi with respect to the x, y, |
269 |
– |
and z components of vectors cr1 and cr2. */ |
270 |
– |
double d_cos_dx_cr1; |
271 |
– |
double d_cos_dy_cr1; |
272 |
– |
double d_cos_dz_cr1; |
273 |
– |
double d_cos_dx_cr2; |
274 |
– |
double d_cos_dy_cr2; |
275 |
– |
double d_cos_dz_cr2; |
276 |
– |
|
277 |
– |
d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr; |
278 |
– |
d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr; |
279 |
– |
d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr; |
280 |
– |
|
281 |
– |
d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr; |
282 |
– |
d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr; |
283 |
– |
d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr; |
284 |
– |
|
285 |
– |
//Vector3d dcosdA = B /(rA * rB) - cos_phi /(rA * rA) * A; |
286 |
– |
//Vector3d dcosdA = 1.0 /rA * (B.normalize() - cos_phi * A.normalize()); |
287 |
– |
//Vector3d dcosdB = 1.0 /rB * (A.normalize() - cos_phi * B.normalize()); |
288 |
– |
|
289 |
– |
/*********************************************************************** |
290 |
– |
* |
291 |
– |
* Calculate the actual forces and place them in the atoms. |
292 |
– |
* |
293 |
– |
***********************************************************************/ |
294 |
– |
|
295 |
– |
double force; /*the force scaling factor */ |
296 |
– |
|
297 |
– |
force = torsion_force(cos_phi); |
298 |
– |
|
299 |
– |
aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y); |
300 |
– |
aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z); |
301 |
– |
aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x); |
302 |
– |
|
303 |
– |
bF[0] = force * ( d_cos_dy_cr1 * (r_ab.z - r_cb.z) |
304 |
– |
- d_cos_dy_cr2 * r_cd.z |
305 |
– |
+ d_cos_dz_cr1 * (r_cb.y - r_ab.y) |
306 |
– |
+ d_cos_dz_cr2 * r_cd.y); |
307 |
– |
bF[1] = force * ( d_cos_dx_cr1 * (r_cb.z - r_ab.z) |
308 |
– |
+ d_cos_dx_cr2 * r_cd.z |
309 |
– |
+ d_cos_dz_cr1 * (r_ab.x - r_cb.x) |
310 |
– |
- d_cos_dz_cr2 * r_cd.x); |
311 |
– |
bF[2] = force * ( d_cos_dx_cr1 * (r_ab.y - r_cb.y) |
312 |
– |
- d_cos_dx_cr2 * r_cd.y |
313 |
– |
+ d_cos_dy_cr1 * (r_cb.x - r_ab.x) |
314 |
– |
+ d_cos_dy_cr2 * r_cd.x); |
315 |
– |
|
316 |
– |
cF[0] = force * (- d_cos_dy_cr1 * r_ab.z |
317 |
– |
- d_cos_dy_cr2 * (r_cb.z - r_cd.z) |
318 |
– |
+ d_cos_dz_cr1 * r_ab.y |
319 |
– |
- d_cos_dz_cr2 * (r_cd.y - r_cb.y)); |
320 |
– |
cF[1] = force * ( d_cos_dx_cr1 * r_ab.z |
321 |
– |
- d_cos_dx_cr2 * (r_cd.z - r_cb.z) |
322 |
– |
- d_cos_dz_cr1 * r_ab.x |
323 |
– |
- d_cos_dz_cr2 * (r_cb.x - r_cd.x)); |
324 |
– |
cF[2] = force * (- d_cos_dx_cr1 * r_ab.y |
325 |
– |
- d_cos_dx_cr2 * (r_cb.y - r_cd.y) |
326 |
– |
+ d_cos_dy_cr1 * r_ab.x |
327 |
– |
- d_cos_dy_cr2 * (r_cd.x - r_cb.x)); |
328 |
– |
|
329 |
– |
dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y); |
330 |
– |
dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z); |
331 |
– |
dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x); |
332 |
– |
|
333 |
– |
|
334 |
– |
c_p_a->addFrc(aF); |
335 |
– |
c_p_b->addFrc(bF); |
336 |
– |
c_p_c->addFrc(cF); |
337 |
– |
c_p_d->addFrc(dF); |
338 |
– |
|
339 |
– |
//double firstDerivative; |
340 |
– |
//bondType_->calcForce(cos_phi, firstDerivative, potential_); |
341 |
– |
//f1 = force * cross (dcosdA, r32); |
342 |
– |
//f2 = |
343 |
– |
//f3 = |
344 |
– |
//f4 = force * cross(dcosdB, r32); |
345 |
– |
//atom1_->addFrc(f1); |
346 |
– |
//atom2_->addFrc(f2); |
347 |
– |
//atom3_->addFrc(f3); |
348 |
– |
//atom4_->addFrc(f4); |
349 |
– |
|
350 |
– |
|
351 |
– |
} |
352 |
– |
|
353 |
– |
} |
354 |
– |
======= |
355 |
– |
#include "primitives/Torsion.hpp" |
356 |
– |
|
357 |
– |
namespace oopse { |
358 |
– |
|
5 |
|
Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
6 |
|
TorsionType *tt) : |
7 |
|
atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { } |
89 |
|
} |
90 |
|
|
91 |
|
} |
446 |
– |
>>>>>>> 1.2.2.4 |