1 |
+ |
/* |
2 |
+ |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
+ |
* |
4 |
+ |
* The University of Notre Dame grants you ("Licensee") a |
5 |
+ |
* non-exclusive, royalty free, license to use, modify and |
6 |
+ |
* redistribute this software in source and binary code form, provided |
7 |
+ |
* that the following conditions are met: |
8 |
+ |
* |
9 |
+ |
* 1. Redistributions of source code must retain the above copyright |
10 |
+ |
* notice, this list of conditions and the following disclaimer. |
11 |
+ |
* |
12 |
+ |
* 2. Redistributions in binary form must reproduce the above copyright |
13 |
+ |
* notice, this list of conditions and the following disclaimer in the |
14 |
+ |
* documentation and/or other materials provided with the |
15 |
+ |
* distribution. |
16 |
+ |
* |
17 |
+ |
* This software is provided "AS IS," without a warranty of any |
18 |
+ |
* kind. All express or implied conditions, representations and |
19 |
+ |
* warranties, including any implied warranty of merchantability, |
20 |
+ |
* fitness for a particular purpose or non-infringement, are hereby |
21 |
+ |
* excluded. The University of Notre Dame and its licensors shall not |
22 |
+ |
* be liable for any damages suffered by licensee as a result of |
23 |
+ |
* using, modifying or distributing the software or its |
24 |
+ |
* derivatives. In no event will the University of Notre Dame or its |
25 |
+ |
* licensors be liable for any lost revenue, profit or data, or for |
26 |
+ |
* direct, indirect, special, consequential, incidental or punitive |
27 |
+ |
* damages, however caused and regardless of the theory of liability, |
28 |
+ |
* arising out of the use of or inability to use software, even if the |
29 |
+ |
* University of Notre Dame has been advised of the possibility of |
30 |
+ |
* such damages. |
31 |
+ |
* |
32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
33 |
+ |
* research, please cite the appropriate papers when you publish your |
34 |
+ |
* work. Good starting points are: |
35 |
+ |
* |
36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
41 |
+ |
*/ |
42 |
+ |
|
43 |
|
#include <math.h> |
44 |
|
#include <iostream> |
3 |
– |
using namespace std; |
45 |
|
|
46 |
|
#ifdef IS_MPI |
47 |
|
#include <mpi.h> |
48 |
|
#endif //is_mpi |
49 |
|
|
50 |
|
#include "brains/Thermo.hpp" |
51 |
< |
#include "primitives/SRI.hpp" |
11 |
< |
#include "integrators/Integrator.hpp" |
51 |
> |
#include "primitives/Molecule.hpp" |
52 |
|
#include "utils/simError.h" |
53 |
< |
#include "math/MatVec3.h" |
53 |
> |
#include "utils/PhysicalConstants.hpp" |
54 |
> |
#include "types/MultipoleAdapter.hpp" |
55 |
|
|
56 |
+ |
namespace OpenMD { |
57 |
+ |
|
58 |
+ |
RealType Thermo::getKinetic() { |
59 |
+ |
SimInfo::MoleculeIterator miter; |
60 |
+ |
std::vector<StuntDouble*>::iterator iiter; |
61 |
+ |
Molecule* mol; |
62 |
+ |
StuntDouble* integrableObject; |
63 |
+ |
Vector3d vel; |
64 |
+ |
Vector3d angMom; |
65 |
+ |
Mat3x3d I; |
66 |
+ |
int i; |
67 |
+ |
int j; |
68 |
+ |
int k; |
69 |
+ |
RealType mass; |
70 |
+ |
RealType kinetic = 0.0; |
71 |
+ |
RealType kinetic_global = 0.0; |
72 |
+ |
|
73 |
+ |
for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) { |
74 |
+ |
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
75 |
+ |
integrableObject = mol->nextIntegrableObject(iiter)) { |
76 |
+ |
|
77 |
+ |
mass = integrableObject->getMass(); |
78 |
+ |
vel = integrableObject->getVel(); |
79 |
+ |
|
80 |
+ |
kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
81 |
+ |
|
82 |
+ |
if (integrableObject->isDirectional()) { |
83 |
+ |
angMom = integrableObject->getJ(); |
84 |
+ |
I = integrableObject->getI(); |
85 |
+ |
|
86 |
+ |
if (integrableObject->isLinear()) { |
87 |
+ |
i = integrableObject->linearAxis(); |
88 |
+ |
j = (i + 1) % 3; |
89 |
+ |
k = (i + 2) % 3; |
90 |
+ |
kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k); |
91 |
+ |
} else { |
92 |
+ |
kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1) |
93 |
+ |
+ angMom[2]*angMom[2]/I(2, 2); |
94 |
+ |
} |
95 |
+ |
} |
96 |
+ |
|
97 |
+ |
} |
98 |
+ |
} |
99 |
+ |
|
100 |
|
#ifdef IS_MPI |
16 |
– |
#define __C |
17 |
– |
#include "brains/mpiSimulation.hpp" |
18 |
– |
#endif // is_mpi |
101 |
|
|
102 |
< |
inline double roundMe( double x ){ |
103 |
< |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
104 |
< |
} |
102 |
> |
MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM, |
103 |
> |
MPI_COMM_WORLD); |
104 |
> |
kinetic = kinetic_global; |
105 |
|
|
106 |
< |
Thermo::Thermo( SimInfo* the_info ) { |
25 |
< |
info = the_info; |
26 |
< |
int baseSeed = the_info->getSeed(); |
27 |
< |
|
28 |
< |
gaussStream = new gaussianSPRNG( baseSeed ); |
29 |
< |
} |
106 |
> |
#endif //is_mpi |
107 |
|
|
108 |
< |
Thermo::~Thermo(){ |
32 |
< |
delete gaussStream; |
33 |
< |
} |
108 |
> |
kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert; |
109 |
|
|
110 |
< |
double Thermo::getKinetic(){ |
110 |
> |
return kinetic; |
111 |
> |
} |
112 |
|
|
113 |
< |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
114 |
< |
double kinetic; |
39 |
< |
double amass; |
40 |
< |
double aVel[3], aJ[3], I[3][3]; |
41 |
< |
int i, j, k, kl; |
113 |
> |
RealType Thermo::getPotential() { |
114 |
> |
RealType potential = 0.0; |
115 |
|
|
116 |
< |
double kinetic_global; |
117 |
< |
vector<StuntDouble *> integrableObjects = info->integrableObjects; |
118 |
< |
|
119 |
< |
kinetic = 0.0; |
47 |
< |
kinetic_global = 0.0; |
116 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
117 |
> |
potential = curSnapshot->getShortRangePotential() + curSnapshot->getLongRangePotential(); |
118 |
> |
return potential; |
119 |
> |
} |
120 |
|
|
121 |
< |
for (kl=0; kl<integrableObjects.size(); kl++) { |
122 |
< |
integrableObjects[kl]->getVel(aVel); |
51 |
< |
amass = integrableObjects[kl]->getMass(); |
121 |
> |
RealType Thermo::getTotalE() { |
122 |
> |
RealType total; |
123 |
|
|
124 |
< |
for(j=0; j<3; j++) |
125 |
< |
kinetic += amass*aVel[j]*aVel[j]; |
124 |
> |
total = this->getKinetic() + this->getPotential(); |
125 |
> |
return total; |
126 |
> |
} |
127 |
|
|
128 |
< |
if (integrableObjects[kl]->isDirectional()){ |
129 |
< |
|
130 |
< |
integrableObjects[kl]->getJ( aJ ); |
131 |
< |
integrableObjects[kl]->getI( I ); |
128 |
> |
RealType Thermo::getTemperature() { |
129 |
> |
|
130 |
> |
RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb ); |
131 |
> |
return temperature; |
132 |
> |
} |
133 |
|
|
134 |
< |
if (integrableObjects[kl]->isLinear()) { |
135 |
< |
i = integrableObjects[kl]->linearAxis(); |
136 |
< |
j = (i+1)%3; |
137 |
< |
k = (i+2)%3; |
138 |
< |
kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k]; |
139 |
< |
} else { |
140 |
< |
for (j=0; j<3; j++) |
141 |
< |
kinetic += aJ[j]*aJ[j] / I[j][j]; |
134 |
> |
RealType Thermo::getElectronicTemperature() { |
135 |
> |
SimInfo::MoleculeIterator miter; |
136 |
> |
std::vector<Atom*>::iterator iiter; |
137 |
> |
Molecule* mol; |
138 |
> |
Atom* atom; |
139 |
> |
RealType cvel; |
140 |
> |
RealType cmass; |
141 |
> |
RealType kinetic = 0.0; |
142 |
> |
RealType kinetic_global = 0.0; |
143 |
> |
|
144 |
> |
for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) { |
145 |
> |
for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL; |
146 |
> |
atom = mol->nextFluctuatingCharge(iiter)) { |
147 |
> |
cmass = atom->getChargeMass(); |
148 |
> |
cvel = atom->getFlucQVel(); |
149 |
> |
|
150 |
> |
kinetic += cmass * cvel * cvel; |
151 |
> |
|
152 |
|
} |
153 |
< |
} |
154 |
< |
} |
153 |
> |
} |
154 |
> |
|
155 |
|
#ifdef IS_MPI |
156 |
< |
MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, |
157 |
< |
MPI_SUM, MPI_COMM_WORLD); |
158 |
< |
kinetic = kinetic_global; |
156 |
> |
|
157 |
> |
MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM, |
158 |
> |
MPI_COMM_WORLD); |
159 |
> |
kinetic = kinetic_global; |
160 |
> |
|
161 |
|
#endif //is_mpi |
77 |
– |
|
78 |
– |
kinetic = kinetic * 0.5 / e_convert; |
162 |
|
|
163 |
< |
return kinetic; |
164 |
< |
} |
163 |
> |
kinetic = kinetic * 0.5; |
164 |
> |
return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb ); |
165 |
> |
} |
166 |
|
|
83 |
– |
double Thermo::getPotential(){ |
84 |
– |
|
85 |
– |
double potential_local; |
86 |
– |
double potential; |
87 |
– |
int el, nSRI; |
88 |
– |
Molecule* molecules; |
167 |
|
|
90 |
– |
molecules = info->molecules; |
91 |
– |
nSRI = info->n_SRI; |
168 |
|
|
93 |
– |
potential_local = 0.0; |
94 |
– |
potential = 0.0; |
95 |
– |
potential_local += info->lrPot; |
169 |
|
|
170 |
< |
for( el=0; el<info->n_mol; el++ ){ |
171 |
< |
potential_local += molecules[el].getPotential(); |
170 |
> |
RealType Thermo::getVolume() { |
171 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
172 |
> |
return curSnapshot->getVolume(); |
173 |
|
} |
174 |
|
|
175 |
< |
// Get total potential for entire system from MPI. |
102 |
< |
#ifdef IS_MPI |
103 |
< |
MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
104 |
< |
MPI_SUM, MPI_COMM_WORLD); |
105 |
< |
#else |
106 |
< |
potential = potential_local; |
107 |
< |
#endif // is_mpi |
175 |
> |
RealType Thermo::getPressure() { |
176 |
|
|
177 |
< |
return potential; |
110 |
< |
} |
177 |
> |
// Relies on the calculation of the full molecular pressure tensor |
178 |
|
|
112 |
– |
double Thermo::getTotalE(){ |
179 |
|
|
180 |
< |
double total; |
180 |
> |
Mat3x3d tensor; |
181 |
> |
RealType pressure; |
182 |
|
|
183 |
< |
total = this->getKinetic() + this->getPotential(); |
117 |
< |
return total; |
118 |
< |
} |
183 |
> |
tensor = getPressureTensor(); |
184 |
|
|
185 |
< |
double Thermo::getTemperature(){ |
185 |
> |
pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
186 |
|
|
187 |
< |
const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
188 |
< |
double temperature; |
124 |
< |
|
125 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
126 |
< |
return temperature; |
127 |
< |
} |
187 |
> |
return pressure; |
188 |
> |
} |
189 |
|
|
190 |
< |
double Thermo::getVolume() { |
190 |
> |
RealType Thermo::getPressure(int direction) { |
191 |
|
|
192 |
< |
return info->boxVol; |
132 |
< |
} |
192 |
> |
// Relies on the calculation of the full molecular pressure tensor |
193 |
|
|
194 |
< |
double Thermo::getPressure() { |
194 |
> |
|
195 |
> |
Mat3x3d tensor; |
196 |
> |
RealType pressure; |
197 |
|
|
198 |
< |
// Relies on the calculation of the full molecular pressure tensor |
137 |
< |
|
138 |
< |
const double p_convert = 1.63882576e8; |
139 |
< |
double press[3][3]; |
140 |
< |
double pressure; |
198 |
> |
tensor = getPressureTensor(); |
199 |
|
|
200 |
< |
this->getPressureTensor(press); |
200 |
> |
pressure = PhysicalConstants::pressureConvert * tensor(direction, direction); |
201 |
|
|
202 |
< |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
202 |
> |
return pressure; |
203 |
> |
} |
204 |
|
|
205 |
< |
return pressure; |
206 |
< |
} |
205 |
> |
Mat3x3d Thermo::getPressureTensor() { |
206 |
> |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
207 |
> |
// routine derived via viral theorem description in: |
208 |
> |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
209 |
> |
Mat3x3d pressureTensor; |
210 |
> |
Mat3x3d p_local(0.0); |
211 |
> |
Mat3x3d p_global(0.0); |
212 |
|
|
213 |
< |
double Thermo::getPressureX() { |
213 |
> |
SimInfo::MoleculeIterator i; |
214 |
> |
std::vector<StuntDouble*>::iterator j; |
215 |
> |
Molecule* mol; |
216 |
> |
StuntDouble* integrableObject; |
217 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
218 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
219 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
220 |
|
|
221 |
< |
// Relies on the calculation of the full molecular pressure tensor |
222 |
< |
|
223 |
< |
const double p_convert = 1.63882576e8; |
224 |
< |
double press[3][3]; |
225 |
< |
double pressureX; |
221 |
> |
RealType mass = integrableObject->getMass(); |
222 |
> |
Vector3d vcom = integrableObject->getVel(); |
223 |
> |
p_local += mass * outProduct(vcom, vcom); |
224 |
> |
} |
225 |
> |
} |
226 |
> |
|
227 |
> |
#ifdef IS_MPI |
228 |
> |
MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
229 |
> |
#else |
230 |
> |
p_global = p_local; |
231 |
> |
#endif // is_mpi |
232 |
|
|
233 |
< |
this->getPressureTensor(press); |
233 |
> |
RealType volume = this->getVolume(); |
234 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
235 |
> |
Mat3x3d stressTensor = curSnapshot->getStressTensor(); |
236 |
|
|
237 |
< |
pressureX = p_convert * press[0][0]; |
237 |
> |
pressureTensor = (p_global + |
238 |
> |
PhysicalConstants::energyConvert * stressTensor)/volume; |
239 |
> |
|
240 |
> |
return pressureTensor; |
241 |
> |
} |
242 |
|
|
161 |
– |
return pressureX; |
162 |
– |
} |
243 |
|
|
244 |
< |
double Thermo::getPressureY() { |
244 |
> |
void Thermo::saveStat(){ |
245 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
246 |
> |
Stats& stat = currSnapshot->statData; |
247 |
> |
|
248 |
> |
stat[Stats::KINETIC_ENERGY] = getKinetic(); |
249 |
> |
stat[Stats::POTENTIAL_ENERGY] = getPotential(); |
250 |
> |
stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ; |
251 |
> |
stat[Stats::TEMPERATURE] = getTemperature(); |
252 |
> |
stat[Stats::PRESSURE] = getPressure(); |
253 |
> |
stat[Stats::VOLUME] = getVolume(); |
254 |
|
|
255 |
< |
// Relies on the calculation of the full molecular pressure tensor |
256 |
< |
|
257 |
< |
const double p_convert = 1.63882576e8; |
258 |
< |
double press[3][3]; |
259 |
< |
double pressureY; |
255 |
> |
Mat3x3d tensor =getPressureTensor(); |
256 |
> |
stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0); |
257 |
> |
stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1); |
258 |
> |
stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2); |
259 |
> |
stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0); |
260 |
> |
stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1); |
261 |
> |
stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2); |
262 |
> |
stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0); |
263 |
> |
stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1); |
264 |
> |
stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2); |
265 |
|
|
266 |
< |
this->getPressureTensor(press); |
266 |
> |
// grab the simulation box dipole moment if specified |
267 |
> |
if (info_->getCalcBoxDipole()){ |
268 |
> |
Vector3d totalDipole = getBoxDipole(); |
269 |
> |
stat[Stats::BOX_DIPOLE_X] = totalDipole(0); |
270 |
> |
stat[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
271 |
> |
stat[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
272 |
> |
} |
273 |
|
|
274 |
< |
pressureY = p_convert * press[1][1]; |
274 |
> |
Globals* simParams = info_->getSimParams(); |
275 |
> |
// grab the heat flux if desired |
276 |
> |
if (simParams->havePrintHeatFlux()) { |
277 |
> |
if (simParams->getPrintHeatFlux()){ |
278 |
> |
Vector3d heatFlux = getHeatFlux(); |
279 |
> |
stat[Stats::HEATFLUX_X] = heatFlux(0); |
280 |
> |
stat[Stats::HEATFLUX_Y] = heatFlux(1); |
281 |
> |
stat[Stats::HEATFLUX_Z] = heatFlux(2); |
282 |
> |
} |
283 |
> |
} |
284 |
|
|
285 |
< |
return pressureY; |
286 |
< |
} |
285 |
> |
if (simParams->haveTaggedAtomPair() && |
286 |
> |
simParams->havePrintTaggedPairDistance()) { |
287 |
> |
if ( simParams->getPrintTaggedPairDistance()) { |
288 |
> |
|
289 |
> |
std::pair<int, int> tap = simParams->getTaggedAtomPair(); |
290 |
> |
Vector3d pos1, pos2, rab; |
291 |
|
|
292 |
< |
double Thermo::getPressureZ() { |
292 |
> |
#ifdef IS_MPI |
293 |
> |
std::cerr << "tap = " << tap.first << " " << tap.second << std::endl; |
294 |
|
|
295 |
< |
// Relies on the calculation of the full molecular pressure tensor |
296 |
< |
|
297 |
< |
const double p_convert = 1.63882576e8; |
184 |
< |
double press[3][3]; |
185 |
< |
double pressureZ; |
295 |
> |
int mol1 = info_->getGlobalMolMembership(tap.first); |
296 |
> |
int mol2 = info_->getGlobalMolMembership(tap.second); |
297 |
> |
std::cerr << "mols = " << mol1 << " " << mol2 << std::endl; |
298 |
|
|
299 |
< |
this->getPressureTensor(press); |
299 |
> |
int proc1 = info_->getMolToProc(mol1); |
300 |
> |
int proc2 = info_->getMolToProc(mol2); |
301 |
|
|
302 |
< |
pressureZ = p_convert * press[2][2]; |
302 |
> |
std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl; |
303 |
|
|
304 |
< |
return pressureZ; |
305 |
< |
} |
304 |
> |
RealType data[3]; |
305 |
> |
if (proc1 == worldRank) { |
306 |
> |
StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first); |
307 |
> |
std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl; |
308 |
> |
pos1 = sd1->getPos(); |
309 |
> |
data[0] = pos1.x(); |
310 |
> |
data[1] = pos1.y(); |
311 |
> |
data[2] = pos1.z(); |
312 |
> |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
313 |
> |
} else { |
314 |
> |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
315 |
> |
pos1 = Vector3d(data); |
316 |
> |
} |
317 |
|
|
318 |
|
|
319 |
< |
void Thermo::getPressureTensor(double press[3][3]){ |
320 |
< |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
321 |
< |
// routine derived via viral theorem description in: |
322 |
< |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
323 |
< |
|
324 |
< |
const double e_convert = 4.184e-4; |
325 |
< |
|
326 |
< |
double molmass, volume; |
327 |
< |
double vcom[3]; |
328 |
< |
double p_local[9], p_global[9]; |
329 |
< |
int i, j, k; |
330 |
< |
|
331 |
< |
for (i=0; i < 9; i++) { |
332 |
< |
p_local[i] = 0.0; |
333 |
< |
p_global[i] = 0.0; |
334 |
< |
} |
335 |
< |
|
336 |
< |
// use velocities of integrableObjects and their masses: |
337 |
< |
|
338 |
< |
for (i=0; i < info->integrableObjects.size(); i++) { |
339 |
< |
|
340 |
< |
molmass = info->integrableObjects[i]->getMass(); |
217 |
< |
|
218 |
< |
info->integrableObjects[i]->getVel(vcom); |
219 |
< |
|
220 |
< |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
221 |
< |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
222 |
< |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
223 |
< |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
224 |
< |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
225 |
< |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
226 |
< |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
227 |
< |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
228 |
< |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
229 |
< |
|
230 |
< |
} |
231 |
< |
|
232 |
< |
// Get total for entire system from MPI. |
233 |
< |
|
234 |
< |
#ifdef IS_MPI |
235 |
< |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
236 |
< |
#else |
237 |
< |
for (i=0; i<9; i++) { |
238 |
< |
p_global[i] = p_local[i]; |
239 |
< |
} |
240 |
< |
#endif // is_mpi |
241 |
< |
|
242 |
< |
volume = this->getVolume(); |
243 |
< |
|
244 |
< |
|
245 |
< |
|
246 |
< |
for(i = 0; i < 3; i++) { |
247 |
< |
for (j = 0; j < 3; j++) { |
248 |
< |
k = 3*i + j; |
249 |
< |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
319 |
> |
if (proc2 == worldRank) { |
320 |
> |
StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second); |
321 |
> |
std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl; |
322 |
> |
pos2 = sd2->getPos(); |
323 |
> |
data[0] = pos2.x(); |
324 |
> |
data[1] = pos2.y(); |
325 |
> |
data[2] = pos2.z(); |
326 |
> |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
327 |
> |
} else { |
328 |
> |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
329 |
> |
pos2 = Vector3d(data); |
330 |
> |
} |
331 |
> |
#else |
332 |
> |
StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first); |
333 |
> |
StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second); |
334 |
> |
pos1 = at1->getPos(); |
335 |
> |
pos2 = at2->getPos(); |
336 |
> |
#endif |
337 |
> |
rab = pos2 - pos1; |
338 |
> |
currSnapshot->wrapVector(rab); |
339 |
> |
stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length(); |
340 |
> |
} |
341 |
|
} |
342 |
+ |
|
343 |
+ |
/**@todo need refactorying*/ |
344 |
+ |
//Conserved Quantity is set by integrator and time is set by setTime |
345 |
+ |
|
346 |
|
} |
252 |
– |
} |
347 |
|
|
254 |
– |
void Thermo::velocitize() { |
255 |
– |
|
256 |
– |
double aVel[3], aJ[3], I[3][3]; |
257 |
– |
int i, j, l, m, n, vr, vd; // velocity randomizer loop counters |
258 |
– |
double vdrift[3]; |
259 |
– |
double vbar; |
260 |
– |
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
261 |
– |
double av2; |
262 |
– |
double kebar; |
263 |
– |
double temperature; |
264 |
– |
int nobj; |
348 |
|
|
349 |
< |
if (!info->have_target_temp) { |
350 |
< |
sprintf( painCave.errMsg, |
351 |
< |
"You can't resample the velocities without a targetTemp!\n" |
352 |
< |
); |
353 |
< |
painCave.isFatal = 1; |
354 |
< |
painCave.severity = OOPSE_ERROR; |
355 |
< |
simError(); |
356 |
< |
return; |
357 |
< |
} |
349 |
> |
Vector3d Thermo::getBoxDipole() { |
350 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
351 |
> |
SimInfo::MoleculeIterator miter; |
352 |
> |
std::vector<Atom*>::iterator aiter; |
353 |
> |
Molecule* mol; |
354 |
> |
Atom* atom; |
355 |
> |
RealType charge; |
356 |
> |
RealType moment(0.0); |
357 |
> |
Vector3d ri(0.0); |
358 |
> |
Vector3d dipoleVector(0.0); |
359 |
> |
Vector3d nPos(0.0); |
360 |
> |
Vector3d pPos(0.0); |
361 |
> |
RealType nChg(0.0); |
362 |
> |
RealType pChg(0.0); |
363 |
> |
int nCount = 0; |
364 |
> |
int pCount = 0; |
365 |
|
|
366 |
< |
nobj = info->integrableObjects.size(); |
367 |
< |
|
368 |
< |
temperature = info->target_temp; |
279 |
< |
|
280 |
< |
kebar = kb * temperature * (double)info->ndfRaw / |
281 |
< |
( 2.0 * (double)info->ndf ); |
282 |
< |
|
283 |
< |
for(vr = 0; vr < nobj; vr++){ |
366 |
> |
RealType chargeToC = 1.60217733e-19; |
367 |
> |
RealType angstromToM = 1.0e-10; |
368 |
> |
RealType debyeToCm = 3.33564095198e-30; |
369 |
|
|
370 |
< |
// uses equipartition theory to solve for vbar in angstrom/fs |
370 |
> |
for (mol = info_->beginMolecule(miter); mol != NULL; |
371 |
> |
mol = info_->nextMolecule(miter)) { |
372 |
|
|
373 |
< |
av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); |
374 |
< |
vbar = sqrt( av2 ); |
373 |
> |
for (atom = mol->beginAtom(aiter); atom != NULL; |
374 |
> |
atom = mol->nextAtom(aiter)) { |
375 |
> |
|
376 |
> |
if (atom->isCharge() ) { |
377 |
> |
charge = 0.0; |
378 |
> |
GenericData* data = atom->getAtomType()->getPropertyByName("Charge"); |
379 |
> |
if (data != NULL) { |
380 |
|
|
381 |
< |
// picks random velocities from a gaussian distribution |
382 |
< |
// centered on vbar |
381 |
> |
charge = (dynamic_cast<DoubleGenericData*>(data))->getData(); |
382 |
> |
charge *= chargeToC; |
383 |
|
|
384 |
< |
for (j=0; j<3; j++) |
385 |
< |
aVel[j] = vbar * gaussStream->getGaussian(); |
384 |
> |
ri = atom->getPos(); |
385 |
> |
currSnapshot->wrapVector(ri); |
386 |
> |
ri *= angstromToM; |
387 |
> |
|
388 |
> |
if (charge < 0.0) { |
389 |
> |
nPos += ri; |
390 |
> |
nChg -= charge; |
391 |
> |
nCount++; |
392 |
> |
} else if (charge > 0.0) { |
393 |
> |
pPos += ri; |
394 |
> |
pChg += charge; |
395 |
> |
pCount++; |
396 |
> |
} |
397 |
> |
} |
398 |
> |
} |
399 |
> |
|
400 |
> |
MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType()); |
401 |
> |
if (ma.isDipole() ) { |
402 |
> |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
403 |
> |
moment = ma.getDipoleMoment(); |
404 |
> |
moment *= debyeToCm; |
405 |
> |
dipoleVector += u_i * moment; |
406 |
> |
} |
407 |
> |
} |
408 |
> |
} |
409 |
|
|
410 |
< |
info->integrableObjects[vr]->setVel( aVel ); |
411 |
< |
|
412 |
< |
if(info->integrableObjects[vr]->isDirectional()){ |
410 |
> |
|
411 |
> |
#ifdef IS_MPI |
412 |
> |
RealType pChg_global, nChg_global; |
413 |
> |
int pCount_global, nCount_global; |
414 |
> |
Vector3d pPos_global, nPos_global, dipVec_global; |
415 |
|
|
416 |
< |
info->integrableObjects[vr]->getI( I ); |
416 |
> |
MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM, |
417 |
> |
MPI_COMM_WORLD); |
418 |
> |
pChg = pChg_global; |
419 |
> |
MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM, |
420 |
> |
MPI_COMM_WORLD); |
421 |
> |
nChg = nChg_global; |
422 |
> |
MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM, |
423 |
> |
MPI_COMM_WORLD); |
424 |
> |
pCount = pCount_global; |
425 |
> |
MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM, |
426 |
> |
MPI_COMM_WORLD); |
427 |
> |
nCount = nCount_global; |
428 |
> |
MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3, |
429 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
430 |
> |
pPos = pPos_global; |
431 |
> |
MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3, |
432 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
433 |
> |
nPos = nPos_global; |
434 |
> |
MPI_Allreduce(dipoleVector.getArrayPointer(), |
435 |
> |
dipVec_global.getArrayPointer(), 3, |
436 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
437 |
> |
dipoleVector = dipVec_global; |
438 |
> |
#endif //is_mpi |
439 |
|
|
440 |
< |
if (info->integrableObjects[vr]->isLinear()) { |
440 |
> |
// first load the accumulated dipole moment (if dipoles were present) |
441 |
> |
Vector3d boxDipole = dipoleVector; |
442 |
> |
// now include the dipole moment due to charges |
443 |
> |
// use the lesser of the positive and negative charge totals |
444 |
> |
RealType chg_value = nChg <= pChg ? nChg : pChg; |
445 |
> |
|
446 |
> |
// find the average positions |
447 |
> |
if (pCount > 0 && nCount > 0 ) { |
448 |
> |
pPos /= pCount; |
449 |
> |
nPos /= nCount; |
450 |
> |
} |
451 |
|
|
452 |
< |
l= info->integrableObjects[vr]->linearAxis(); |
453 |
< |
m = (l+1)%3; |
306 |
< |
n = (l+2)%3; |
452 |
> |
// dipole is from the negative to the positive (physics notation) |
453 |
> |
boxDipole += (pPos - nPos) * chg_value; |
454 |
|
|
455 |
< |
aJ[l] = 0.0; |
309 |
< |
vbar = sqrt( 2.0 * kebar * I[m][m] ); |
310 |
< |
aJ[m] = vbar * gaussStream->getGaussian(); |
311 |
< |
vbar = sqrt( 2.0 * kebar * I[n][n] ); |
312 |
< |
aJ[n] = vbar * gaussStream->getGaussian(); |
313 |
< |
|
314 |
< |
} else { |
315 |
< |
for (j = 0 ; j < 3; j++) { |
316 |
< |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
317 |
< |
aJ[j] = vbar * gaussStream->getGaussian(); |
318 |
< |
} |
319 |
< |
} // else isLinear |
320 |
< |
|
321 |
< |
info->integrableObjects[vr]->setJ( aJ ); |
322 |
< |
|
323 |
< |
}//isDirectional |
324 |
< |
|
455 |
> |
return boxDipole; |
456 |
|
} |
457 |
|
|
458 |
< |
// Get the Center of Mass drift velocity. |
458 |
> |
// Returns the Heat Flux Vector for the system |
459 |
> |
Vector3d Thermo::getHeatFlux(){ |
460 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
461 |
> |
SimInfo::MoleculeIterator miter; |
462 |
> |
std::vector<StuntDouble*>::iterator iiter; |
463 |
> |
Molecule* mol; |
464 |
> |
StuntDouble* integrableObject; |
465 |
> |
RigidBody::AtomIterator ai; |
466 |
> |
Atom* atom; |
467 |
> |
Vector3d vel; |
468 |
> |
Vector3d angMom; |
469 |
> |
Mat3x3d I; |
470 |
> |
int i; |
471 |
> |
int j; |
472 |
> |
int k; |
473 |
> |
RealType mass; |
474 |
|
|
475 |
< |
getCOMVel(vdrift); |
476 |
< |
|
477 |
< |
// Corrects for the center of mass drift. |
478 |
< |
// sums all the momentum and divides by total mass. |
475 |
> |
Vector3d x_a; |
476 |
> |
RealType kinetic; |
477 |
> |
RealType potential; |
478 |
> |
RealType eatom; |
479 |
> |
RealType AvgE_a_ = 0; |
480 |
> |
// Convective portion of the heat flux |
481 |
> |
Vector3d heatFluxJc = V3Zero; |
482 |
|
|
483 |
< |
for(vd = 0; vd < nobj; vd++){ |
484 |
< |
|
485 |
< |
info->integrableObjects[vd]->getVel(aVel); |
486 |
< |
|
487 |
< |
for (j=0; j < 3; j++) |
488 |
< |
aVel[j] -= vdrift[j]; |
483 |
> |
/* Calculate convective portion of the heat flux */ |
484 |
> |
for (mol = info_->beginMolecule(miter); mol != NULL; |
485 |
> |
mol = info_->nextMolecule(miter)) { |
486 |
> |
|
487 |
> |
for (integrableObject = mol->beginIntegrableObject(iiter); |
488 |
> |
integrableObject != NULL; |
489 |
> |
integrableObject = mol->nextIntegrableObject(iiter)) { |
490 |
|
|
491 |
< |
info->integrableObjects[vd]->setVel( aVel ); |
492 |
< |
} |
491 |
> |
mass = integrableObject->getMass(); |
492 |
> |
vel = integrableObject->getVel(); |
493 |
|
|
494 |
< |
} |
494 |
> |
kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
495 |
> |
|
496 |
> |
if (integrableObject->isDirectional()) { |
497 |
> |
angMom = integrableObject->getJ(); |
498 |
> |
I = integrableObject->getI(); |
499 |
|
|
500 |
< |
void Thermo::getCOMVel(double vdrift[3]){ |
500 |
> |
if (integrableObject->isLinear()) { |
501 |
> |
i = integrableObject->linearAxis(); |
502 |
> |
j = (i + 1) % 3; |
503 |
> |
k = (i + 2) % 3; |
504 |
> |
kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k); |
505 |
> |
} else { |
506 |
> |
kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1) |
507 |
> |
+ angMom[2]*angMom[2]/I(2, 2); |
508 |
> |
} |
509 |
> |
} |
510 |
|
|
511 |
< |
double mtot, mtot_local; |
349 |
< |
double aVel[3], amass; |
350 |
< |
double vdrift_local[3]; |
351 |
< |
int vd, j; |
352 |
< |
int nobj; |
511 |
> |
potential = 0.0; |
512 |
|
|
513 |
< |
nobj = info->integrableObjects.size(); |
513 |
> |
if (integrableObject->isRigidBody()) { |
514 |
> |
RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject); |
515 |
> |
for (atom = rb->beginAtom(ai); atom != NULL; |
516 |
> |
atom = rb->nextAtom(ai)) { |
517 |
> |
potential += atom->getParticlePot(); |
518 |
> |
} |
519 |
> |
} else { |
520 |
> |
potential = integrableObject->getParticlePot(); |
521 |
> |
cerr << "ppot = " << potential << "\n"; |
522 |
> |
} |
523 |
|
|
524 |
< |
mtot_local = 0.0; |
525 |
< |
vdrift_local[0] = 0.0; |
526 |
< |
vdrift_local[1] = 0.0; |
527 |
< |
vdrift_local[2] = 0.0; |
528 |
< |
|
529 |
< |
for(vd = 0; vd < nobj; vd++){ |
530 |
< |
|
531 |
< |
amass = info->integrableObjects[vd]->getMass(); |
364 |
< |
info->integrableObjects[vd]->getVel( aVel ); |
524 |
> |
potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2 |
525 |
> |
// The potential may not be a 1/2 factor |
526 |
> |
eatom = (kinetic + potential)/2.0; // amu A^2/fs^2 |
527 |
> |
heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3 |
528 |
> |
heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3 |
529 |
> |
heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3 |
530 |
> |
} |
531 |
> |
} |
532 |
|
|
533 |
< |
for(j = 0; j < 3; j++) |
367 |
< |
vdrift_local[j] += aVel[j] * amass; |
368 |
< |
|
369 |
< |
mtot_local += amass; |
370 |
< |
} |
533 |
> |
std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl; |
534 |
|
|
535 |
+ |
/* The J_v vector is reduced in fortan so everyone has the global |
536 |
+ |
* Jv. Jc is computed over the local atoms and must be reduced |
537 |
+ |
* among all processors. |
538 |
+ |
*/ |
539 |
|
#ifdef IS_MPI |
540 |
< |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
541 |
< |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
375 |
< |
#else |
376 |
< |
mtot = mtot_local; |
377 |
< |
for(vd = 0; vd < 3; vd++) { |
378 |
< |
vdrift[vd] = vdrift_local[vd]; |
379 |
< |
} |
540 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE, |
541 |
> |
MPI::SUM); |
542 |
|
#endif |
543 |
|
|
544 |
< |
for (vd = 0; vd < 3; vd++) { |
383 |
< |
vdrift[vd] = vdrift[vd] / mtot; |
384 |
< |
} |
385 |
< |
|
386 |
< |
} |
544 |
> |
// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3 |
545 |
|
|
546 |
< |
void Thermo::getCOM(double COM[3]){ |
547 |
< |
|
390 |
< |
double mtot, mtot_local; |
391 |
< |
double aPos[3], amass; |
392 |
< |
double COM_local[3]; |
393 |
< |
int i, j; |
394 |
< |
int nobj; |
395 |
< |
|
396 |
< |
mtot_local = 0.0; |
397 |
< |
COM_local[0] = 0.0; |
398 |
< |
COM_local[1] = 0.0; |
399 |
< |
COM_local[2] = 0.0; |
400 |
< |
|
401 |
< |
nobj = info->integrableObjects.size(); |
402 |
< |
for(i = 0; i < nobj; i++){ |
546 |
> |
Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() * |
547 |
> |
PhysicalConstants::energyConvert; |
548 |
|
|
549 |
< |
amass = info->integrableObjects[i]->getMass(); |
550 |
< |
info->integrableObjects[i]->getPos( aPos ); |
406 |
< |
|
407 |
< |
for(j = 0; j < 3; j++) |
408 |
< |
COM_local[j] += aPos[j] * amass; |
549 |
> |
std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl; |
550 |
> |
std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl; |
551 |
|
|
552 |
< |
mtot_local += amass; |
552 |
> |
// Correct for the fact the flux is 1/V (Jc + Jv) |
553 |
> |
return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3 |
554 |
|
} |
555 |
< |
|
413 |
< |
#ifdef IS_MPI |
414 |
< |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
415 |
< |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
416 |
< |
#else |
417 |
< |
mtot = mtot_local; |
418 |
< |
for(i = 0; i < 3; i++) { |
419 |
< |
COM[i] = COM_local[i]; |
420 |
< |
} |
421 |
< |
#endif |
422 |
< |
|
423 |
< |
for (i = 0; i < 3; i++) { |
424 |
< |
COM[i] = COM[i] / mtot; |
425 |
< |
} |
426 |
< |
} |
427 |
< |
|
428 |
< |
void Thermo::removeCOMdrift() { |
429 |
< |
double vdrift[3], aVel[3]; |
430 |
< |
int vd, j, nobj; |
431 |
< |
|
432 |
< |
nobj = info->integrableObjects.size(); |
433 |
< |
|
434 |
< |
// Get the Center of Mass drift velocity. |
435 |
< |
|
436 |
< |
getCOMVel(vdrift); |
437 |
< |
|
438 |
< |
// Corrects for the center of mass drift. |
439 |
< |
// sums all the momentum and divides by total mass. |
440 |
< |
|
441 |
< |
for(vd = 0; vd < nobj; vd++){ |
442 |
< |
|
443 |
< |
info->integrableObjects[vd]->getVel(aVel); |
444 |
< |
|
445 |
< |
for (j=0; j < 3; j++) |
446 |
< |
aVel[j] -= vdrift[j]; |
447 |
< |
|
448 |
< |
info->integrableObjects[vd]->setVel( aVel ); |
449 |
< |
} |
450 |
< |
} |
555 |
> |
} //end namespace OpenMD |