src/brains/Thermo.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include <math.h>
#include <iostream>

#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

#include "brains/Thermo.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {

  RealType Thermo::getKinetic() {
    SimInfo::MoleculeIterator miter;
    std::vector<StuntDouble*>::iterator iiter;
    Molecule* mol;
    StuntDouble* integrableObject;    
    Vector3d vel;
    Vector3d angMom;
    Mat3x3d I;
    int i;
    int j;
    int k;
    RealType mass;
    RealType kinetic = 0.0;
    RealType kinetic_global = 0.0;
    
    for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(iiter)) {
        
        mass = integrableObject->getMass();
        vel = integrableObject->getVel();
        
        kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
        
        if (integrableObject->isDirectional()) {
          angMom = integrableObject->getJ();
          I = integrableObject->getI();

          if (integrableObject->isLinear()) {
            i = integrableObject->linearAxis();
            j = (i + 1) % 3;
            k = (i + 2) % 3;
            kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
          } else {                        
            kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1) 
              + angMom[2]*angMom[2]/I(2, 2);
          }
        }
            
      }
    }
    
#ifdef IS_MPI

    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
    kinetic = kinetic_global;

#endif //is_mpi

    kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;

    return kinetic;
  }

  RealType Thermo::getPotential() {
    RealType potential = 0.0;
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;

    // Get total potential for entire system from MPI.

#ifdef IS_MPI

    MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
    potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];

#else

    potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];

#endif // is_mpi

    return potential;
  }

  RealType Thermo::getTotalE() {
    RealType total;

    total = this->getKinetic() + this->getPotential();
    return total;
  }

  RealType Thermo::getTemperature() {
    
    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
    return temperature;
  }

  RealType Thermo::getVolume() { 
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    return curSnapshot->getVolume();
  }

  RealType Thermo::getPressure() {

    // Relies on the calculation of the full molecular pressure tensor


    Mat3x3d tensor;
    RealType pressure;

    tensor = getPressureTensor();

    pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;

    return pressure;
  }

  RealType Thermo::getPressure(int direction) {

    // Relies on the calculation of the full molecular pressure tensor

          
    Mat3x3d tensor;
    RealType pressure;

    tensor = getPressureTensor();

    pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);

    return pressure;
  }

  Mat3x3d Thermo::getPressureTensor() {
    // returns pressure tensor in units amu*fs^-2*Ang^-1
    // routine derived via viral theorem description in:
    // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
    Mat3x3d pressureTensor;
    Mat3x3d p_local(0.0);
    Mat3x3d p_global(0.0);

    SimInfo::MoleculeIterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;    
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(j)) {

        RealType mass = integrableObject->getMass();
        Vector3d vcom = integrableObject->getVel();
        p_local += mass * outProduct(vcom, vcom);         
      }
    }
    
#ifdef IS_MPI
    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#else
    p_global = p_local;
#endif // is_mpi

    RealType volume = this->getVolume();
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    Mat3x3d tau = curSnapshot->statData.getTau();

    pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
    
    return pressureTensor;
  }


  void Thermo::saveStat(){
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    Stats& stat = currSnapshot->statData;
    
    stat[Stats::KINETIC_ENERGY] = getKinetic();
    stat[Stats::POTENTIAL_ENERGY] = getPotential();
    stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
    stat[Stats::TEMPERATURE] = getTemperature();
    stat[Stats::PRESSURE] = getPressure();
    stat[Stats::VOLUME] = getVolume();      

    Mat3x3d tensor =getPressureTensor();
    stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);      
    stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);      
    stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);      
    stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);      
    stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);      
    stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);      
    stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);      
    stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);      
    stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);      


    Globals* simParams = info_->getSimParams();

    if (simParams->haveTaggedAtomPair() && 
        simParams->havePrintTaggedPairDistance()) {
      if ( simParams->getPrintTaggedPairDistance()) {
        
        std::pair<int, int> tap = simParams->getTaggedAtomPair();
        Vector3d pos1, pos2, rab;

#ifdef IS_MPI        
        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;

        int mol1 = info_->getGlobalMolMembership(tap.first);
        int mol2 = info_->getGlobalMolMembership(tap.second);
        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;

        int proc1 = info_->getMolToProc(mol1);
        int proc2 = info_->getMolToProc(mol2);

        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;

        RealType data[3];
        if (proc1 == worldRank) {
          StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
          std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
          pos1 = sd1->getPos();
          data[0] = pos1.x();
          data[1] = pos1.y();
          data[2] = pos1.z();          
          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
        } else {
          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
          pos1 = Vector3d(data);
        }


        if (proc2 == worldRank) {
          StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
          std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
          pos2 = sd2->getPos();
          data[0] = pos2.x();
          data[1] = pos2.y();
          data[2] = pos2.z();          
          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
        } else {
          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
          pos2 = Vector3d(data);
        }
#else
        StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
        StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
        pos1 = at1->getPos();
        pos2 = at2->getPos();
#endif        
        rab = pos2 - pos1;
        currSnapshot->wrapVector(rab);
        stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
      }
    }
      
    /**@todo need refactorying*/
    //Conserved Quantity is set by integrator and time is set by setTime
    
  }

} //end namespace OpenMD
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
File size:	10353 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	Content
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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include <math.h>
43	#include <iostream>
44
45	#ifdef IS_MPI
46	#include <mpi.h>
47	#endif //is_mpi
48
49	#include "brains/Thermo.hpp"
50	#include "primitives/Molecule.hpp"
51	#include "utils/simError.h"
52	#include "utils/PhysicalConstants.hpp"
53
54	namespace OpenMD {
55
56	RealType Thermo::getKinetic() {
57	SimInfo::MoleculeIterator miter;
58	std::vector<StuntDouble*>::iterator iiter;
59	Molecule* mol;
60	StuntDouble* integrableObject;
61	Vector3d vel;
62	Vector3d angMom;
63	Mat3x3d I;
64	int i;
65	int j;
66	int k;
67	RealType mass;
68	RealType kinetic = 0.0;
69	RealType kinetic_global = 0.0;
70
71	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73	integrableObject = mol->nextIntegrableObject(iiter)) {
74
75	mass = integrableObject->getMass();
76	vel = integrableObject->getVel();
77
78	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
79
80	if (integrableObject->isDirectional()) {
81	angMom = integrableObject->getJ();
82	I = integrableObject->getI();
83
84	if (integrableObject->isLinear()) {
85	i = integrableObject->linearAxis();
86	j = (i + 1) % 3;
87	k = (i + 2) % 3;
88	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
89	} else {
90	kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
91	+ angMom[2]*angMom[2]/I(2, 2);
92	}
93	}
94
95	}
96	}
97
98	#ifdef IS_MPI
99
100	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	MPI_COMM_WORLD);
102	kinetic = kinetic_global;
103
104	#endif //is_mpi
105
106	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
107
108	return kinetic;
109	}
110
111	RealType Thermo::getPotential() {
112	RealType potential = 0.0;
113	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115
116	// Get total potential for entire system from MPI.
117
118	#ifdef IS_MPI
119
120	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	MPI_COMM_WORLD);
122	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123
124	#else
125
126	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127
128	#endif // is_mpi
129
130	return potential;
131	}
132
133	RealType Thermo::getTotalE() {
134	RealType total;
135
136	total = this->getKinetic() + this->getPotential();
137	return total;
138	}
139
140	RealType Thermo::getTemperature() {
141
142	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143	return temperature;
144	}
145
146	RealType Thermo::getVolume() {
147	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148	return curSnapshot->getVolume();
149	}
150
151	RealType Thermo::getPressure() {
152
153	// Relies on the calculation of the full molecular pressure tensor
154
155
156	Mat3x3d tensor;
157	RealType pressure;
158
159	tensor = getPressureTensor();
160
161	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162
163	return pressure;
164	}
165
166	RealType Thermo::getPressure(int direction) {
167
168	// Relies on the calculation of the full molecular pressure tensor
169
170
171	Mat3x3d tensor;
172	RealType pressure;
173
174	tensor = getPressureTensor();
175
176	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
177
178	return pressure;
179	}
180
181	Mat3x3d Thermo::getPressureTensor() {
182	// returns pressure tensor in units amufs^-2Ang^-1
183	// routine derived via viral theorem description in:
184	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
185	Mat3x3d pressureTensor;
186	Mat3x3d p_local(0.0);
187	Mat3x3d p_global(0.0);
188
189	SimInfo::MoleculeIterator i;
190	std::vector<StuntDouble*>::iterator j;
191	Molecule* mol;
192	StuntDouble* integrableObject;
193	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195	integrableObject = mol->nextIntegrableObject(j)) {
196
197	RealType mass = integrableObject->getMass();
198	Vector3d vcom = integrableObject->getVel();
199	p_local += mass * outProduct(vcom, vcom);
200	}
201	}
202
203	#ifdef IS_MPI
204	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205	#else
206	p_global = p_local;
207	#endif // is_mpi
208
209	RealType volume = this->getVolume();
210	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211	Mat3x3d tau = curSnapshot->statData.getTau();
212
213	pressureTensor = (p_global + PhysicalConstants::energyConvert* tau)/volume;
214
215	return pressureTensor;
216	}
217
218
219	void Thermo::saveStat(){
220	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221	Stats& stat = currSnapshot->statData;
222
223	stat[Stats::KINETIC_ENERGY] = getKinetic();
224	stat[Stats::POTENTIAL_ENERGY] = getPotential();
225	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
226	stat[Stats::TEMPERATURE] = getTemperature();
227	stat[Stats::PRESSURE] = getPressure();
228	stat[Stats::VOLUME] = getVolume();
229
230	Mat3x3d tensor =getPressureTensor();
231	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
232	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
233	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
234	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
235	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
236	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
237	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
238	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
239	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
240
241
242	Globals* simParams = info_->getSimParams();
243
244	if (simParams->haveTaggedAtomPair() &&
245	simParams->havePrintTaggedPairDistance()) {
246	if ( simParams->getPrintTaggedPairDistance()) {
247
248	std::pair<int, int> tap = simParams->getTaggedAtomPair();
249	Vector3d pos1, pos2, rab;
250
251	#ifdef IS_MPI
252	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
253
254	int mol1 = info_->getGlobalMolMembership(tap.first);
255	int mol2 = info_->getGlobalMolMembership(tap.second);
256	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
257
258	int proc1 = info_->getMolToProc(mol1);
259	int proc2 = info_->getMolToProc(mol2);
260
261	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
262
263	RealType data[3];
264	if (proc1 == worldRank) {
265	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
266	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
267	pos1 = sd1->getPos();
268	data[0] = pos1.x();
269	data[1] = pos1.y();
270	data[2] = pos1.z();
271	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
272	} else {
273	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
274	pos1 = Vector3d(data);
275	}
276
277
278	if (proc2 == worldRank) {
279	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
280	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
281	pos2 = sd2->getPos();
282	data[0] = pos2.x();
283	data[1] = pos2.y();
284	data[2] = pos2.z();
285	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
286	} else {
287	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
288	pos2 = Vector3d(data);
289	}
290	#else
291	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
292	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
293	pos1 = at1->getPos();
294	pos2 = at2->getPos();
295	#endif
296	rab = pos2 - pos1;
297	currSnapshot->wrapVector(rab);
298	stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length();
299	}
300	}
301
302	/*@todo need refactorying/
303	//Conserved Quantity is set by integrator and time is set by setTime
304
305	}
306
307	} //end namespace OpenMD