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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
27 |
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28 |
< |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
29 |
< |
T( theInfo, the_ff ) |
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{ |
28 |
> |
NPTf::NPTf (SimInfo* info): NPT(info){ |
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GenericData* data; |
30 |
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DoubleVectorGenericData * etaValue; |
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int i,j; |
33 |
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for(i = 0; i < 3; i++){ |
34 |
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for (j = 0; j < 3; j++){ |
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|
36 |
< |
eta[i][j] = 0.0; |
37 |
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oldEta[i][j] = 0.0; |
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eta(i, j) = 0.0; |
37 |
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oldEta(i, j) = 0.0; |
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} |
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} |
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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eta[i][j] = (*etaValue)[3*i+j]; |
53 |
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oldEta[i][j] = eta[i][j]; |
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eta(i, j) = (*etaValue)[3*i+j]; |
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oldEta(i, j) = eta(i, j); |
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} |
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} |
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} |
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} |
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template<typename T> NPTf<T>::~NPTf() { |
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NPTf::~NPTf() { |
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// empty for now |
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} |
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template<typename T> void NPTf<T>::resetIntegrator() { |
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void NPTf::evolveEtaA() { |
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int i, j; |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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|
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T::resetIntegrator(); |
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} |
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|
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template<typename T> void NPTf<T>::evolveEtaA() { |
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|
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int i, j; |
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|
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for(i = 0; i < 3; i ++){ |
85 |
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for(j = 0; j < 3; j++){ |
86 |
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if( i == j) |
87 |
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eta[i][j] += dt2 * instaVol * |
88 |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
89 |
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else |
90 |
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
71 |
> |
for(i = 0; i < 3; i ++){ |
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> |
for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/p_convert) / (NkBT*tb2); |
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> |
} else { |
76 |
> |
eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); |
77 |
> |
} |
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> |
} |
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} |
92 |
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} |
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< |
for(i = 0; i < 3; i++) |
82 |
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for (j = 0; j < 3; j++) |
83 |
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oldEta[i][j] = eta[i][j]; |
81 |
> |
for(i = 0; i < 3; i++) { |
82 |
> |
for (j = 0; j < 3; j++) { |
83 |
> |
oldEta(i, j) = eta(i, j); |
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} |
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} |
86 |
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|
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} |
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|
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template<typename T> void NPTf<T>::evolveEtaB() { |
89 |
> |
void NPTf::evolveEtaB() { |
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|
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int i,j; |
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int i; |
92 |
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int j; |
93 |
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|
94 |
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for(i = 0; i < 3; i++) |
95 |
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for (j = 0; j < 3; j++) |
96 |
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prevEta[i][j] = eta[i][j]; |
94 |
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for(i = 0; i < 3; i++) { |
95 |
> |
for (j = 0; j < 3; j++) { |
96 |
> |
prevEta(i, j) = eta(i, j); |
97 |
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} |
98 |
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} |
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|
100 |
< |
for(i = 0; i < 3; i ++){ |
101 |
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for(j = 0; j < 3; j++){ |
102 |
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if( i == j) { |
103 |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
104 |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
105 |
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} else { |
106 |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
107 |
< |
} |
100 |
> |
for(i = 0; i < 3; i ++){ |
101 |
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for(j = 0; j < 3; j++){ |
102 |
> |
if( i == j) { |
103 |
> |
eta(i, j) = oldEta(i, j) + dt2 * instaVol * |
104 |
> |
(press(i, j) - targetPressure/p_convert) / (NkBT*tb2); |
105 |
> |
} else { |
106 |
> |
eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); |
107 |
> |
} |
108 |
> |
} |
109 |
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} |
110 |
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} |
110 |
> |
|
111 |
> |
|
112 |
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} |
113 |
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|
114 |
< |
template<typename T> void NPTf<T>::calcVelScale(void){ |
120 |
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int i,j; |
114 |
> |
void NPTf::calcVelScale(){ |
115 |
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|
116 |
< |
for (i = 0; i < 3; i++ ) { |
117 |
< |
for (j = 0; j < 3; j++ ) { |
118 |
< |
vScale[i][j] = eta[i][j]; |
116 |
> |
for (int i = 0; i < 3; i++ ) { |
117 |
> |
for (int j = 0; j < 3; j++ ) { |
118 |
> |
vScale(i, j) = eta(i, j); |
119 |
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|
120 |
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if (i == j) { |
121 |
< |
vScale[i][j] += chi; |
121 |
> |
vScale(i, j) += chi; |
122 |
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} |
123 |
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} |
124 |
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} |
125 |
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} |
126 |
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|
127 |
< |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
128 |
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|
135 |
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matVecMul3( vScale, vel, sc ); |
127 |
> |
void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel);{ |
128 |
> |
sc = vScale * vel; |
129 |
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} |
130 |
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|
131 |
< |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
132 |
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int j; |
140 |
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double myVel[3]; |
141 |
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|
142 |
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for (j = 0; j < 3; j++) |
143 |
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myVel[j] = oldVel[3*index + j]; |
144 |
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|
145 |
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matVecMul3( vScale, myVel, sc ); |
131 |
> |
void NPTf::getVelScaleB(Vector3d& sc, int index ) { |
132 |
> |
sc = vScale * oldVel[index]; |
133 |
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} |
134 |
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|
135 |
< |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
136 |
< |
int index, double sc[3]){ |
150 |
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int j; |
151 |
< |
double rj[3]; |
135 |
> |
void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, |
136 |
> |
int index, Vector3d& sc) { |
137 |
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|
138 |
< |
for(j=0; j<3; j++) |
139 |
< |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
140 |
< |
|
156 |
< |
matVecMul3( eta, rj, sc ); |
138 |
> |
/**@todo */ |
139 |
> |
Vector3d rj = (oldPos[index] + pos[j])/2.0 -COM; |
140 |
> |
sc = eta * rj; |
141 |
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} |
142 |
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|
143 |
< |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
143 |
> |
void NPTf::scaleSimBox(){ |
144 |
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|
145 |
< |
int i,j,k; |
146 |
< |
double scaleMat[3][3]; |
145 |
> |
int i; |
146 |
> |
int j; |
147 |
> |
int k; |
148 |
> |
Mat3x3d scaleMat; |
149 |
|
double eta2ij; |
150 |
|
double bigScale, smallScale, offDiagMax; |
151 |
< |
double hm[3][3], hmnew[3][3]; |
151 |
> |
Mat3x3d hm; |
152 |
> |
Mat3x3d hmnew; |
153 |
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|
154 |
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|
155 |
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|
170 |
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|
171 |
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eta2ij = 0.0; |
172 |
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for(k=0; k<3; k++){ |
173 |
< |
eta2ij += eta[i][k] * eta[k][j]; |
173 |
> |
eta2ij += eta(i, k) * eta(k, j); |
174 |
|
} |
175 |
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|
176 |
< |
scaleMat[i][j] = 0.0; |
176 |
> |
scaleMat(i, j) = 0.0; |
177 |
|
// identity matrix (see above): |
178 |
< |
if (i == j) scaleMat[i][j] = 1.0; |
178 |
> |
if (i == j) scaleMat(i, j) = 1.0; |
179 |
|
// Taylor expansion for the exponential truncated at second order: |
180 |
< |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
180 |
> |
scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
181 |
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|
182 |
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|
183 |
|
if (i != j) |
184 |
< |
if (fabs(scaleMat[i][j]) > offDiagMax) |
185 |
< |
offDiagMax = fabs(scaleMat[i][j]); |
184 |
> |
if (fabs(scaleMat(i, j)) > offDiagMax) |
185 |
> |
offDiagMax = fabs(scaleMat(i, j)); |
186 |
|
} |
187 |
|
|
188 |
< |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
189 |
< |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
188 |
> |
if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
189 |
> |
if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
190 |
|
} |
191 |
|
|
192 |
|
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
199 |
|
" eta = [%lf\t%lf\t%lf]\n" |
200 |
|
" [%lf\t%lf\t%lf]\n" |
201 |
|
" [%lf\t%lf\t%lf]\n", |
202 |
< |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
203 |
< |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
204 |
< |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
205 |
< |
eta[0][0],eta[0][1],eta[0][2], |
206 |
< |
eta[1][0],eta[1][1],eta[1][2], |
207 |
< |
eta[2][0],eta[2][1],eta[2][2]); |
202 |
> |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
203 |
> |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
204 |
> |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
205 |
> |
eta(0, 0),eta(0, 1),eta(0, 2), |
206 |
> |
eta(1, 0),eta(1, 1),eta(1, 2), |
207 |
> |
eta(2, 0),eta(2, 1),eta(2, 2)); |
208 |
|
painCave.isFatal = 1; |
209 |
|
simError(); |
210 |
|
} else if (offDiagMax > 0.01) { |
217 |
|
" eta = [%lf\t%lf\t%lf]\n" |
218 |
|
" [%lf\t%lf\t%lf]\n" |
219 |
|
" [%lf\t%lf\t%lf]\n", |
220 |
< |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
221 |
< |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
222 |
< |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
223 |
< |
eta[0][0],eta[0][1],eta[0][2], |
224 |
< |
eta[1][0],eta[1][1],eta[1][2], |
225 |
< |
eta[2][0],eta[2][1],eta[2][2]); |
220 |
> |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
221 |
> |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
222 |
> |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
223 |
> |
eta(0, 0),eta(0, 1),eta(0, 2), |
224 |
> |
eta(1, 0),eta(1, 1),eta(1, 2), |
225 |
> |
eta(2, 0),eta(2, 1),eta(2, 2)); |
226 |
|
painCave.isFatal = 1; |
227 |
|
simError(); |
228 |
|
} else { |
232 |
|
} |
233 |
|
} |
234 |
|
|
235 |
< |
template<typename T> bool NPTf<T>::etaConverged() { |
236 |
< |
int i; |
237 |
< |
double diffEta, sumEta; |
235 |
> |
bool NPTf::etaConverged() { |
236 |
> |
int i; |
237 |
> |
double diffEta, sumEta; |
238 |
|
|
239 |
< |
sumEta = 0; |
240 |
< |
for(i = 0; i < 3; i++) |
241 |
< |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
239 |
> |
sumEta = 0; |
240 |
> |
for(i = 0; i < 3; i++) { |
241 |
> |
sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
242 |
> |
} |
243 |
> |
|
244 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
245 |
|
|
246 |
< |
diffEta = sqrt( sumEta / 3.0 ); |
257 |
< |
|
258 |
< |
return ( diffEta <= etaTolerance ); |
246 |
> |
return ( diffEta <= etaTolerance ); |
247 |
|
} |
248 |
|
|
249 |
< |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
249 |
> |
double NPTf::calcConservedQuantity(){ |
250 |
|
|
251 |
< |
double conservedQuantity; |
252 |
< |
double totalEnergy; |
253 |
< |
double thermostat_kinetic; |
254 |
< |
double thermostat_potential; |
255 |
< |
double barostat_kinetic; |
256 |
< |
double barostat_potential; |
257 |
< |
double trEta; |
270 |
< |
double a[3][3], b[3][3]; |
251 |
> |
double conservedQuantity; |
252 |
> |
double totalEnergy; |
253 |
> |
double thermostat_kinetic; |
254 |
> |
double thermostat_potential; |
255 |
> |
double barostat_kinetic; |
256 |
> |
double barostat_potential; |
257 |
> |
double trEta; |
258 |
|
|
259 |
< |
totalEnergy = tStats->getTotalE(); |
259 |
> |
totalEnergy = tStats->getTotalE(); |
260 |
|
|
261 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
275 |
< |
(2.0 * eConvert); |
261 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * eConvert); |
262 |
|
|
263 |
< |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
263 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
264 |
|
|
265 |
< |
transposeMat3(eta, a); |
266 |
< |
matMul3(a, eta, b); |
267 |
< |
trEta = matTrace3(b); |
265 |
> |
trEta = (eta.transpose() * eta).trace(); |
266 |
> |
|
267 |
> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * eConvert); |
268 |
|
|
269 |
< |
barostat_kinetic = NkBT * tb2 * trEta / |
284 |
< |
(2.0 * eConvert); |
269 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /eConvert; |
270 |
|
|
271 |
< |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
272 |
< |
eConvert; |
271 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
272 |
> |
barostat_kinetic + barostat_potential; |
273 |
|
|
274 |
< |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
290 |
< |
barostat_kinetic + barostat_potential; |
274 |
> |
return conservedQuantity; |
275 |
|
|
292 |
– |
return conservedQuantity; |
293 |
– |
|
276 |
|
} |
277 |
|
|
296 |
– |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
297 |
– |
string parameters; |
298 |
– |
const int BUFFERSIZE = 2000; // size of the read buffer |
299 |
– |
char buffer[BUFFERSIZE]; |
300 |
– |
|
301 |
– |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
302 |
– |
parameters += buffer; |
303 |
– |
|
304 |
– |
for(int i = 0; i < 3; i++){ |
305 |
– |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
306 |
– |
parameters += buffer; |
307 |
– |
} |
308 |
– |
|
309 |
– |
return parameters; |
310 |
– |
|
311 |
– |
} |