1 |
+ |
#include <cmath> |
2 |
|
#include "Atom.hpp" |
3 |
|
#include "SRI.hpp" |
4 |
|
#include "AbstractClasses.hpp" |
20 |
|
// |
21 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
22 |
|
|
23 |
< |
NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
24 |
< |
Integrator( theInfo, the_ff ) |
23 |
> |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
24 |
> |
T( theInfo, the_ff ) |
25 |
|
{ |
26 |
|
chi = 0.0; |
27 |
|
eta = 0.0; |
31 |
|
have_target_pressure = 0; |
32 |
|
} |
33 |
|
|
34 |
< |
void NPTi::moveA() { |
34 |
> |
template<typename T> void NPTi<T>::moveA() { |
35 |
|
|
36 |
< |
int i,j,k; |
36 |
< |
int atomIndex, aMatIndex; |
36 |
> |
int i, j; |
37 |
|
DirectionalAtom* dAtom; |
38 |
< |
double Tb[3]; |
39 |
< |
double ji[3]; |
38 |
> |
double Tb[3], ji[3]; |
39 |
> |
double A[3][3], I[3][3]; |
40 |
> |
double angle, mass; |
41 |
> |
double vel[3], pos[3], frc[3]; |
42 |
> |
|
43 |
|
double rj[3]; |
44 |
|
double instaTemp, instaPress, instaVol; |
45 |
< |
double tt2, tb2; |
43 |
< |
double angle; |
45 |
> |
double tt2, tb2, scaleFactor; |
46 |
|
|
47 |
|
tt2 = tauThermostat * tauThermostat; |
48 |
|
tb2 = tauBarostat * tauBarostat; |
51 |
|
instaPress = tStats->getPressure(); |
52 |
|
instaVol = tStats->getVolume(); |
53 |
|
|
54 |
< |
// first evolve chi a half step |
54 |
> |
// first evolve chi a half step |
55 |
|
|
56 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
57 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
57 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
58 |
> |
(p_convert*NkBT*tb2)); |
59 |
|
|
60 |
|
for( i=0; i<nAtoms; i++ ){ |
61 |
< |
atomIndex = i * 3; |
62 |
< |
aMatIndex = i * 9; |
63 |
< |
|
61 |
< |
// velocity half step |
62 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
63 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
64 |
< |
- vel[j]*(chi+eta)); |
61 |
> |
atoms[i]->getVel( vel ); |
62 |
> |
atoms[i]->getPos( pos ); |
63 |
> |
atoms[i]->getFrc( frc ); |
64 |
|
|
65 |
< |
// position whole step |
65 |
> |
mass = atoms[i]->getMass(); |
66 |
|
|
67 |
< |
for( j=atomIndex; j<(atomIndex+3); j=j+3 ) { |
68 |
< |
rj[0] = pos[j]; |
69 |
< |
rj[1] = pos[j+1]; |
70 |
< |
rj[2] = pos[j+2]; |
67 |
> |
for (j=0; j < 3; j++) { |
68 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
69 |
> |
rj[j] = pos[j]; |
70 |
> |
} |
71 |
|
|
72 |
< |
info->wrapVector(rj); |
72 |
> |
atoms[i]->setVel( vel ); |
73 |
|
|
74 |
< |
pos[j] += dt * (vel[j] + eta*rj[0]); |
76 |
< |
pos[j+1] += dt * (vel[j+1] + eta*rj[1]); |
77 |
< |
pos[j+2] += dt * (vel[j+2] + eta*rj[2]); |
78 |
< |
} |
74 |
> |
info->wrapVector(rj); |
75 |
|
|
76 |
< |
// Scale the box after all the positions have been moved: |
76 |
> |
for (j = 0; j < 3; j++) |
77 |
> |
pos[j] += dt * (vel[j] + eta*rj[j]); |
78 |
|
|
79 |
< |
info->scaleBox(exp(dt*eta)); |
80 |
< |
|
79 |
> |
atoms[i]->setPos( pos ); |
80 |
> |
|
81 |
|
if( atoms[i]->isDirectional() ){ |
82 |
|
|
83 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
84 |
|
|
85 |
|
// get and convert the torque to body frame |
86 |
|
|
87 |
< |
Tb[0] = dAtom->getTx(); |
91 |
< |
Tb[1] = dAtom->getTy(); |
92 |
< |
Tb[2] = dAtom->getTz(); |
93 |
< |
|
87 |
> |
dAtom->getTrq( Tb ); |
88 |
|
dAtom->lab2Body( Tb ); |
89 |
|
|
90 |
|
// get the angular momentum, and propagate a half step |
91 |
|
|
92 |
< |
ji[0] = dAtom->getJx(); |
93 |
< |
ji[1] = dAtom->getJy(); |
94 |
< |
ji[2] = dAtom->getJz(); |
92 |
> |
dAtom->getJ( ji ); |
93 |
> |
|
94 |
> |
for (j=0; j < 3; j++) |
95 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
96 |
|
|
102 |
– |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
103 |
– |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
104 |
– |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
105 |
– |
|
97 |
|
// use the angular velocities to propagate the rotation matrix a |
98 |
|
// full time step |
99 |
< |
|
99 |
> |
|
100 |
> |
dAtom->getA(A); |
101 |
> |
dAtom->getI(I); |
102 |
> |
|
103 |
|
// rotate about the x-axis |
104 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
105 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
106 |
< |
|
104 |
> |
angle = dt2 * ji[0] / I[0][0]; |
105 |
> |
this->rotate( 1, 2, angle, ji, A ); |
106 |
> |
|
107 |
|
// rotate about the y-axis |
108 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
109 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
108 |
> |
angle = dt2 * ji[1] / I[1][1]; |
109 |
> |
this->rotate( 2, 0, angle, ji, A ); |
110 |
|
|
111 |
|
// rotate about the z-axis |
112 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
113 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
112 |
> |
angle = dt * ji[2] / I[2][2]; |
113 |
> |
this->rotate( 0, 1, angle, ji, A); |
114 |
|
|
115 |
|
// rotate about the y-axis |
116 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
117 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
116 |
> |
angle = dt2 * ji[1] / I[1][1]; |
117 |
> |
this->rotate( 2, 0, angle, ji, A ); |
118 |
|
|
119 |
|
// rotate about the x-axis |
120 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
121 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
120 |
> |
angle = dt2 * ji[0] / I[0][0]; |
121 |
> |
this->rotate( 1, 2, angle, ji, A ); |
122 |
|
|
123 |
< |
dAtom->setJx( ji[0] ); |
124 |
< |
dAtom->setJy( ji[1] ); |
125 |
< |
dAtom->setJz( ji[2] ); |
126 |
< |
} |
133 |
< |
|
123 |
> |
dAtom->setJ( ji ); |
124 |
> |
dAtom->setA( A ); |
125 |
> |
} |
126 |
> |
|
127 |
|
} |
128 |
+ |
|
129 |
+ |
// Scale the box after all the positions have been moved: |
130 |
+ |
|
131 |
+ |
scaleFactor = exp(dt*eta); |
132 |
+ |
|
133 |
+ |
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
134 |
+ |
sprintf( painCave.errMsg, |
135 |
+ |
"NPTi error: Attempting a Box scaling of more than 10 percent" |
136 |
+ |
" check your tauBarostat, as it is probably too small!\n" |
137 |
+ |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
138 |
+ |
); |
139 |
+ |
painCave.isFatal = 1; |
140 |
+ |
simError(); |
141 |
+ |
} else { |
142 |
+ |
info->scaleBox(exp(dt*eta)); |
143 |
+ |
} |
144 |
+ |
|
145 |
|
} |
146 |
|
|
147 |
< |
void NPTi::moveB( void ){ |
148 |
< |
int i,j,k; |
149 |
< |
int atomIndex; |
147 |
> |
template<typename T> void NPTi<T>::moveB( void ){ |
148 |
> |
|
149 |
> |
int i, j; |
150 |
|
DirectionalAtom* dAtom; |
151 |
< |
double Tb[3]; |
152 |
< |
double ji[3]; |
151 |
> |
double Tb[3], ji[3]; |
152 |
> |
double vel[3], frc[3]; |
153 |
> |
double mass; |
154 |
> |
|
155 |
|
double instaTemp, instaPress, instaVol; |
156 |
|
double tt2, tb2; |
157 |
|
|
163 |
|
instaVol = tStats->getVolume(); |
164 |
|
|
165 |
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
166 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
166 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
167 |
> |
(p_convert*NkBT*tb2)); |
168 |
|
|
169 |
|
for( i=0; i<nAtoms; i++ ){ |
170 |
< |
atomIndex = i * 3; |
171 |
< |
|
170 |
> |
|
171 |
> |
atoms[i]->getVel( vel ); |
172 |
> |
atoms[i]->getFrc( frc ); |
173 |
> |
|
174 |
> |
mass = atoms[i]->getMass(); |
175 |
> |
|
176 |
|
// velocity half step |
177 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
178 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
162 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
163 |
< |
- vel[j]*(chi+eta)); |
177 |
> |
for (j=0; j < 3; j++) |
178 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
179 |
|
|
180 |
+ |
atoms[i]->setVel( vel ); |
181 |
+ |
|
182 |
|
if( atoms[i]->isDirectional() ){ |
183 |
< |
|
183 |
> |
|
184 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
185 |
< |
|
186 |
< |
// get and convert the torque to body frame |
187 |
< |
|
188 |
< |
Tb[0] = dAtom->getTx(); |
172 |
< |
Tb[1] = dAtom->getTy(); |
173 |
< |
Tb[2] = dAtom->getTz(); |
174 |
< |
|
185 |
> |
|
186 |
> |
// get and convert the torque to body frame |
187 |
> |
|
188 |
> |
dAtom->getTrq( Tb ); |
189 |
|
dAtom->lab2Body( Tb ); |
190 |
< |
|
191 |
< |
// get the angular momentum, and complete the angular momentum |
192 |
< |
// half step |
193 |
< |
|
194 |
< |
ji[0] = dAtom->getJx(); |
195 |
< |
ji[1] = dAtom->getJy(); |
196 |
< |
ji[2] = dAtom->getJz(); |
197 |
< |
|
198 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
185 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
186 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
187 |
< |
|
188 |
< |
dAtom->setJx( ji[0] ); |
189 |
< |
dAtom->setJy( ji[1] ); |
190 |
< |
dAtom->setJz( ji[2] ); |
190 |
> |
|
191 |
> |
// get the angular momentum, and propagate a half step |
192 |
> |
|
193 |
> |
dAtom->getJ( ji ); |
194 |
> |
|
195 |
> |
for (j=0; j < 3; j++) |
196 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
197 |
> |
|
198 |
> |
dAtom->setJ( ji ); |
199 |
|
} |
200 |
|
} |
201 |
|
} |
202 |
|
|
203 |
< |
int NPTi::readyCheck() { |
203 |
> |
template<typename T> int NPTi<T>::readyCheck() { |
204 |
> |
|
205 |
> |
//check parent's readyCheck() first |
206 |
> |
if (T::readyCheck() == -1) |
207 |
> |
return -1; |
208 |
|
|
209 |
|
// First check to see if we have a target temperature. |
210 |
|
// Not having one is fatal. |